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Wu X, Tang J, Cheng B. Oral squamous cell carcinoma gene patterns connected with RNA methylation for prognostic prediction. Oral Dis 2024; 30:408-421. [PMID: 35934835 DOI: 10.1111/odi.14341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/29/2022] [Accepted: 08/01/2022] [Indexed: 11/28/2022]
Abstract
OBJECTIVES To determine whether m6A/m1A/m5C/m7G/m6Am/Ψ-related genes influence the prognosis of a patient with oral squamous cell carcinoma. MATERIALS AND METHODS We investigated the changes in regulatory genes using publicly available data from The Cancer Genome Atlas. Consensus clustering by RNA methylation-related regulators was used to describe oral squamous cell carcinomas (OSCCs). Then, we developed the prediction model. The tumor microenvironment was investigated using ESTIMATE. Gene set enrichment analysis was used to determine whether pathways or cell types were enriched in different groups. The association between the model and immune-related risk scores was investigated using correlation analysis. RESULTS We found 22 gene signatures in this analysis and then developed a predictive model that reveals the genes that are highly connected to the overall survival of OSCC patients. The survival and death rates were substantially different in the two groups (high and low risk) classified by the risk scores. The validation cohort verified the phenotypic diversity and prognostic effects of these genes. CONCLUSION Our data reveal that immune cell infiltration, genetic mutation, and survival potential in OSCC patients are linked to m6A/m1A/m5C/m7G/m6Am/Ψ-related genes, and we constructed a dependable prognostic model for OSCC patients.
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Affiliation(s)
- Xuechen Wu
- Department of Stomatology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jiezhang Tang
- Department of Plastic and Reconstructive Surgery, Xijing Hospital, Fourth Military Medical University, China
| | - Bo Cheng
- Department of Stomatology, Zhongnan Hospital of Wuhan University, Wuhan, China
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Liu L, Zhou Y, Lei X. RMDGCN: Prediction of RNA methylation and disease associations based on graph convolutional network with attention mechanism. PLoS Comput Biol 2023; 19:e1011677. [PMID: 38055721 DOI: 10.1371/journal.pcbi.1011677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 11/10/2023] [Indexed: 12/08/2023] Open
Abstract
RNA modification is a post transcriptional modification that occurs in all organisms and plays a crucial role in the stages of RNA life, closely related to many life processes. As one of the newly discovered modifications, N1-methyladenosine (m1A) plays an important role in gene expression regulation, closely related to the occurrence and development of diseases. However, due to the low abundance of m1A, verifying the associations between m1As and diseases through wet experiments requires a great quantity of manpower and resources. In this study, we proposed a computational method for predicting the associations of RNA methylation and disease based on graph convolutional network (RMDGCN) with attention mechanism. We build an adjacency matrix through the collected m1As and diseases associations, and use positive-unlabeled learning to increase the number of positive samples. By extracting the features of m1As and diseases, a heterogeneous network is constructed, and a GCN with attention mechanism is adopted to predict the associations between m1As and diseases. The experimental results indicate that under a 5-fold cross validation, RMDGCN is superior to other methods (AUC = 0.9892 and AUPR = 0.8682). In addition, case studies indicate that RMDGCN can predict the relationships between unknown m1As and diseases. In summary, RMDGCN is an effective method for predicting the associations between m1As and diseases.
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Affiliation(s)
- Lian Liu
- School of Computer Science, Shaanxi Normal University, Xi'an, Shaanxi, China
| | - Yumeng Zhou
- School of Computer Science, Shaanxi Normal University, Xi'an, Shaanxi, China
| | - Xiujuan Lei
- School of Computer Science, Shaanxi Normal University, Xi'an, Shaanxi, China
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Benak D, Kolar F, Zhang L, Devaux Y, Hlavackova M. RNA modification m 6Am: the role in cardiac biology. Epigenetics 2023; 18:2218771. [PMID: 37331009 DOI: 10.1080/15592294.2023.2218771] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/20/2023] Open
Abstract
Epitranscriptomic modifications have recently emerged into the spotlight of researchers due to their vast regulatory effects on gene expression and thereby cellular physiology and pathophysiology. N6,2'-O-dimethyladenosine (m6Am) is one of the most prevalent chemical marks on RNA and is dynamically regulated by writers (PCIF1, METTL4) and erasers (FTO). The presence or absence of m6Am in RNA affects mRNA stability, regulates transcription, and modulates pre-mRNA splicing. Nevertheless, its functions in the heart are poorly known. This review summarizes the current knowledge and gaps about m6Am modification and its regulators in cardiac biology. It also points out technical challenges and lists the currently available techniques to measure m6Am. A better understanding of epitranscriptomic modifications is needed to improve our knowledge of the molecular regulations in the heart which may lead to novel cardioprotective strategies.
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Affiliation(s)
- Daniel Benak
- Laboratory of Developmental Cardiology, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Physiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Frantisek Kolar
- Laboratory of Developmental Cardiology, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Lu Zhang
- Bioinformatics Platform, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Marketa Hlavackova
- Laboratory of Developmental Cardiology, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
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Xia Y, Zhang Y, Huang J, Chen B, Jiang Y, Sun Z, Liu Y. N6-Methyladenosine Modifications in Pulmonary Hypertension. Pharmacology 2023; 108:497-503. [PMID: 37742623 DOI: 10.1159/000533588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 08/10/2023] [Indexed: 09/26/2023]
Abstract
BACKGROUND The most prevalent kind of RNA methylation modification existing in eukaryotes is N6-methyladenosine (m6A), which is a reversible type of posttranscriptional modification. SUMMARY Many studies have reported that m6A participates in cell differentiation, self-renewal, invasion, and apoptosis by modifying protein synthesis. Furthermore, m6A modification is also involved in disease progression and pulmonary vascular remodeling in pulmonary hypertension. However, very few researchers have investigated the effect of m6A modifications on pulmonary hypertension. KEY MESSAGES Here, we have reviewed the latest research advances in the field of m6A RNA methylation in pulmonary hypertension and explored its regulatory role in pulmonary hypertension development and progression.
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Affiliation(s)
- Yu Xia
- Department of Pharmacy, The Affiliated Lianyungang Hospital of Xuzhou Medical University, Lianyungang, China,
| | - Yanyan Zhang
- Department of Geriatrics, The Affiliated Lianyungang Hospital of Xuzhou Medical University, Lianyungang, China
| | - Jie Huang
- Department of Pharmacy, The Affiliated Lianyungang Hospital of Xuzhou Medical University, Lianyungang, China
| | - Bing Chen
- Department of Pharmacy, The Affiliated Lianyungang Hospital of Xuzhou Medical University, Lianyungang, China
| | - YanJiao Jiang
- Department of Pharmacy, The Affiliated Lianyungang Hospital of Xuzhou Medical University, Lianyungang, China
| | - Zengxian Sun
- Department of Pharmacy, The Affiliated Lianyungang Hospital of Xuzhou Medical University, Lianyungang, China
| | - Yun Liu
- Department of Pharmacy, The Affiliated Lianyungang Hospital of Xuzhou Medical University, Lianyungang, China
- Department of Pharmacy, Lianyungang Clinical College of Nanjing Medical University, Lianyungang, China
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5
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Gao G, Chen A, Gong J, Lin W, Wu W, Mohammad Ismail Hajary S, Lian G, Luo L, Xie L. Comprehensive analyses of m6A RNA methylation patterns and related immune microenvironment in idiopathic pulmonary arterial hypertension. Front Genet 2023; 14:1222368. [PMID: 37732317 PMCID: PMC10507408 DOI: 10.3389/fgene.2023.1222368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 08/18/2023] [Indexed: 09/22/2023] Open
Abstract
Idiopathic pulmonary arterial hypertension (IPAH) is a life-threatening disease with a poor prognosis and high heritability, characterized by elevated pulmonary vascular resistance (PVR) and pulmonary artery pressure. N6-methyladenosine (m6A) RNA modification influences many RNA metabolism pathways. However, the position of m6A methylation regulators in IPAH remains unknown. Therefore, the study aims to disclose the function m6A regulators exert in the pathological mechanisms of IPAH and the immune microenvironment involved. The GSE117261 dataset was downloaded from the Gene Expression Omnibus (GEO) to screen the differentially expressed genes (DEGs) between normal and IPAH samples. Functional and pathway enrichment analyses of DEGs were then conducted by Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG). We also identified the differentially-expressed m6A (DEm6A) regulators between normal and IPAH samples. Key m6A regulators related to the prediction of IPAH were selected using the random forest model. The results showed that FMR1, RBM15, HNRNPA2B1 and IGFBP3 were upregulated in IPAH. In contrast, LRPPRC was downregulated. The single sample gene set enrichment analysis (ssGSEA) method was then adopted to estimate the immune microenvironment in distinct m6A clusters and m6A phenotype-related genes (PRGs) clusters, respectively. Furthermore, we calculated the m6A score via principal component analysis (PCA), and the Sankey diagram was selected to present the correlation among the m6A clusters, m6A PRGs clusters and m6A score. Finally, quantitative RT-PCR and Western blotting were used to validate the key genes in human pulmonary artery smooth muscle cells (HPASMCs) treated by human platelet-derived growth factor-BB (PDGF-BB). The relative mRNA and protein expression levels of FMR1 were significantly elevated, however, the relative mRNA and protein expression levels of LRPPRC were downregulated. Besides, the relative mRNA level of HNRNPA2B1 was increased. Generally, this bioinformatics analysis might provoke more insights into diagnosing and treating IPAH.
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Affiliation(s)
- Gufeng Gao
- Department of Geriatrics, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou, China
- Fujian Hypertension Research Institute, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou, China
- Clinical Research Center for Geriatric Hypertension Disease of Fujian Province, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou, China
- Branch of National Clinical Research Center for Aging and Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Geriatrics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fujian, Fuzhou, China
| | - Ai Chen
- Department of Geriatrics, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou, China
- Fujian Hypertension Research Institute, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou, China
- Clinical Research Center for Geriatric Hypertension Disease of Fujian Province, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou, China
- Branch of National Clinical Research Center for Aging and Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Geriatrics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fujian, Fuzhou, China
| | - Jin Gong
- Department of Geriatrics, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou, China
- Fujian Hypertension Research Institute, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou, China
- Clinical Research Center for Geriatric Hypertension Disease of Fujian Province, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou, China
- Branch of National Clinical Research Center for Aging and Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Geriatrics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fujian, Fuzhou, China
| | - Weijun Lin
- Department of Geriatrics, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou, China
- Fujian Hypertension Research Institute, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou, China
- Clinical Research Center for Geriatric Hypertension Disease of Fujian Province, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou, China
- Branch of National Clinical Research Center for Aging and Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Geriatrics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fujian, Fuzhou, China
| | - Weibin Wu
- Department of Geriatrics, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou, China
- Fujian Hypertension Research Institute, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou, China
- Clinical Research Center for Geriatric Hypertension Disease of Fujian Province, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou, China
- Branch of National Clinical Research Center for Aging and Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Geriatrics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fujian, Fuzhou, China
| | - Sagor Mohammad Ismail Hajary
- Department of Geriatrics, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou, China
- Fujian Hypertension Research Institute, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou, China
- Clinical Research Center for Geriatric Hypertension Disease of Fujian Province, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou, China
- Branch of National Clinical Research Center for Aging and Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Geriatrics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fujian, Fuzhou, China
| | - Guili Lian
- Department of Geriatrics, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou, China
- Fujian Hypertension Research Institute, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou, China
- Clinical Research Center for Geriatric Hypertension Disease of Fujian Province, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou, China
- Branch of National Clinical Research Center for Aging and Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Geriatrics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fujian, Fuzhou, China
| | - Li Luo
- Department of Geriatrics, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou, China
- Fujian Hypertension Research Institute, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou, China
- Clinical Research Center for Geriatric Hypertension Disease of Fujian Province, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou, China
- Branch of National Clinical Research Center for Aging and Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Geriatrics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fujian, Fuzhou, China
| | - Liangdi Xie
- Department of Geriatrics, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou, China
- Fujian Hypertension Research Institute, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou, China
- Clinical Research Center for Geriatric Hypertension Disease of Fujian Province, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou, China
- Branch of National Clinical Research Center for Aging and Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Geriatrics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fujian, Fuzhou, China
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Chen K, Shi Y, Zhu H. Analysis of the role of glucose metabolism-related genes in dilated cardiomyopathy based on bioinformatics. J Thorac Dis 2023; 15:3870-3884. [PMID: 37559624 PMCID: PMC10407475 DOI: 10.21037/jtd-23-906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 07/12/2023] [Indexed: 08/11/2023]
Abstract
BACKGROUND Dilated cardiomyopathy (DCM) is a prevalent condition with diverse etiologies, including viral infection, autoimmune response, and genetic factors. Despite the crucial role of energy metabolism in cardiac function, therapeutic targets for key genes in DCM's energy metabolism remain scarce. METHODS Our study employed the GSE79962 and GSE42955 datasets from the Gene Expression Omnibus (GEO) database for myocardial tissue sample collection and target gene identification via differential gene expression screening. Using various R packages, GSEA software, and the STRING database, we conducted data analysis, gene set enrichment, and protein-protein interaction predictions. The least absolute shrinkage and selection operator (LASSO) and Support Vector Machine (SVM) algorithms aided in feature gene selection, while the predictive model's efficiency was evaluated via the receiver operating characteristic (ROC) curve analysis. We used the non-negative matrix factorization (NMF) method for molecular typing and the cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT) algorithm for predicting immune cell infiltration. RESULTS The DLAT and LDHA genes may regulate the immune microenvironment of DCM by influencing activated dendritic cells, activated mast cells, and M0 macrophages, respectively. The BPGM, DLAT, PGM2, ADH1A, ADH1C, LDHA, and PFKM genes may regulate m6A methylation in DCM by affecting the ZC3H13, ALKBH5, RBMX, HNRNPC, METTL3, and YTHDC1 genes. Further regulatory mechanism analysis suggested that PFKM, DLAT, PKLR, PGM2, LDHA, BPGM, ADH1A, and ADH1C could be involved in the development of cardiomyopathy by regulating the Toll-like receptor signaling pathway. CONCLUSIONS PFKM, DLAT, PKLR, PGM2, LDHA, BPGM, ADH1A, and ADH1C may serve as potential targets for guiding the diagnosis, treatment, and follow-up of DCM.
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Affiliation(s)
- Keping Chen
- Department of Emergency, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Yan Shi
- Operating Room, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Haijie Zhu
- Department of Emergency, Affiliated Hospital of Jiangnan University, Wuxi, China
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Xue Q, Huang Y, Cheng C, Wang Y, Liao F, Duan Q, Wang X, Miao C. Progress in epigenetic regulation of milk synthesis, with particular emphasis on mRNA regulation and DNA methylation. Cell Cycle 2023; 22:1675-1693. [PMID: 37409592 PMCID: PMC10446801 DOI: 10.1080/15384101.2023.2225939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/29/2023] [Accepted: 05/26/2023] [Indexed: 07/07/2023] Open
Abstract
Inadequate milk secretion and a lack of nutrients in humans and mammals are serious problems. It is of great significance to clarify the mechanisms of milk synthesis and treatment methods. Epigenetic modification, represented by RNA methylation, is an important way of gene expression regulation that profoundly affects human gene expression and participates in various physiological and pathological mechanisms. Epigenetic disorders also have an important impact on the production and secretion of milk. This review systematically summarized the research results of epigenetics in the process of lactation in PubMed, Web of Science, NSTL, and other databases and reviewed the effects of epigenetics on human and mammalian lactation, including miRNAs, circRNAs, lncRNAs, DNA methylations, and RNA methylations. The abnormal expression of miRNAs was closely related to the synthesis and secretion of milk fat, milk protein, and other nutrients in the milk of cattle, sheep, and other mammals. MiRNAs are also involved in the synthesis of human milk and the secretion of nutrients. CircRNAs and lncRNAs mainly target miRNAs and regulate the synthesis of nutrients in milk by ceRNA mechanisms. The abnormal expression of DNA and RNA methylation also has an important impact on milk synthesis. Epigenetic modification has the potential to regulate the milk synthesis of breast epithelial cells. Analyzing the mechanisms of human and mammalian milk secretion deficiency and nutrient deficiency from the perspective of epigenetics will provide a new perspective for the treatment of postpartum milk deficiency in pregnant women and mammalian milk secretion deficiency.
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Affiliation(s)
- Qiuyun Xue
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Yurong Huang
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Chenglong Cheng
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Yuting Wang
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Faxue Liao
- The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Public Health Clinical Center, Hefei, China
| | - Qiangjun Duan
- Department of Experimental (Practical Training) Teaching Center, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, 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, Hefei, China
- Institute of Rheumatism, Anhui University of Chinese Medicine, Hefei, China
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8
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Song B, Xie B, Liu M, Li H, Shi D, Zhao F. Bibliometric and visual analysis of RAN methylation in cardiovascular disease. Front Cardiovasc Med 2023; 10:1110718. [PMID: 37063953 PMCID: PMC10098125 DOI: 10.3389/fcvm.2023.1110718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 03/07/2023] [Indexed: 03/31/2023] Open
Abstract
BackgroundRNA methylation is associated with cardiovascular disease (CVD) occurrence and development. The purpose of this study is to visually analyze the results and research trends of global RNA methylation in CVD.MethodsArticles and reviews on RNA methylation in CVD published before 6 November 2022 were searched in the Web of Science Core Collection. Visual and statistical analysis was performed using CiteSpace 1.6.R4 advanced and VOSviewer 1.6.18.ResultsThere were 847 papers from 1,188 institutions and 63 countries/regions. Over approximately 30 years, there was a gradual increase in publications and citations on RNA methylation in CVD. America and China had the highest output (284 and 259 papers, respectively). Nine of the top 20 institutions that published articles were from China, among which Fudan University represented the most. The International Journal of Molecular Sciences was the journal with the most studies. Nature was the most co-cited journal. The most influential writers were Zhang and Wang from China and Mathiyalagan from the United States. After 2015, the primary keywords were cardiac development, heart, promoter methylation, RNA methylation, and N6-methyladenosine. Nuclear RNA, m6A methylation, inhibition, and myocardial infarction were the most common burst keywords from 2020 to the present.ConclusionsA bibliometric analysis reveals research hotspots and trends of RNA methylation in CVD. The regulatory mechanisms of RNA methylation related to CVD and the clinical application of their results, especially m6A methylation, are likely to be the focus of future research.
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Affiliation(s)
- Boce Song
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Beili Xie
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Mingwang Liu
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Haohao Li
- Graduate School, Beijing University of Chinese Medicine, Beijing, China
| | - Dazhuo Shi
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- National Clinical Research Center for Chinese Medicine Cardiology, Beijing, China
| | - Fuhai Zhao
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- National Clinical Research Center for Chinese Medicine Cardiology, Beijing, China
- Correspondence: Fuhai Zhao
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9
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Yu PL, Wu R, Cao SJ, Wen YP, Huang XB, Zhao S, Lang YF, Zhao Q, Lin JC, Du SY, Yu SM, Yan QG. Pseudorabies virus exploits N 6-methyladenosine modification to promote viral replication. Front Microbiol 2023; 14:1087484. [PMID: 36819040 PMCID: PMC9936159 DOI: 10.3389/fmicb.2023.1087484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
Introduction Pseudorabies virus (PRV) is the pathogenic virus of porcine pseudorabies (PR), belonging to the Herpesviridae family. PRV has a wide range of hosts and in recent years has also been reported to infect humans. N6-methyladenosine (m6A) modification is the major pathway of RNA post-transcriptional modification. Whether m6A modification participates in the regulation of PRV replication is unknown. Methods Here, we investigated that the m6A modification was abundant in the PRV transcripts and PRV infection affected the epitranscriptome of host cells. Knockdown of cellular m6A methyltransferases METTL3 and METTL14 and the specific binding proteins YTHDF2 and YTHDF3 inhibited PRV replication, while silencing of demethylase ALKBH5 promoted PRV output. The overexpression of METTL14 induced more efficient virus proliferation in PRV-infected PK15 cells. Inhibition of m6A modification by 3-deazaadenosine (3-DAA), a m6A modification inhibitor, could significantly reduce viral replication. Results and Discussion Taken together, m6A modification played a positive role in the regulation of PRV replication and gene expression. Our research revealed m6A modification sites in PRV transcripts and determined that m6A modification dynamically mediated the interaction between PRV and host.
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Affiliation(s)
- Pei-Lun Yu
- Department of Preventive Veterinary Medicine, Swine Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Rui Wu
- Department of Preventive Veterinary Medicine, Swine Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - San-Jie Cao
- Department of Preventive Veterinary Medicine, Swine Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yi-Ping Wen
- Department of Preventive Veterinary Medicine, Swine Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xiao-Bo Huang
- Department of Preventive Veterinary Medicine, Swine Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shan Zhao
- Department of Preventive Veterinary Medicine, Swine Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yi-Fei Lang
- Department of Preventive Veterinary Medicine, Swine Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qin Zhao
- Department of Preventive Veterinary Medicine, Swine Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Ju-Chun Lin
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Sen-Yan Du
- Department of Preventive Veterinary Medicine, Swine Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shu-Min Yu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qi-Gui Yan
- Department of Preventive Veterinary Medicine, Swine Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,*Correspondence: Qi-Gui Yan, ✉
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10
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Pan W, Jie W, Huang H. Vascular calcification: Molecular mechanisms and therapeutic interventions. MedComm (Beijing) 2023; 4:e200. [PMID: 36620697 PMCID: PMC9811665 DOI: 10.1002/mco2.200] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 01/05/2023] Open
Abstract
Vascular calcification (VC) is recognized as a pathological vascular disorder associated with various diseases, such as atherosclerosis, hypertension, aortic valve stenosis, coronary artery disease, diabetes mellitus, as well as chronic kidney disease. Therefore, it is a life-threatening state for human health. There were several studies targeting mechanisms of VC that revealed the importance of vascular smooth muscle cells transdifferentiating, phosphorous and calcium milieu, as well as matrix vesicles on the progress of VC. However, the underlying molecular mechanisms of VC need to be elucidated. Though there is no acknowledged effective therapeutic strategy to reverse or cure VC clinically, recent evidence has proved that VC is not a passive irreversible comorbidity but an active process regulated by many factors. Some available approaches targeting the underlying molecular mechanism provide promising prospects for the therapy of VC. This review aims to summarize the novel findings on molecular mechanisms and therapeutic interventions of VC, including the role of inflammatory responses, endoplasmic reticulum stress, mitochondrial dysfunction, iron homeostasis, metabolic imbalance, and some related signaling pathways on VC progression. We also conclude some recent studies on controversial interventions in the clinical practice of VC, such as calcium channel blockers, renin-angiotensin system inhibitions, statins, bisphosphonates, denosumab, vitamins, and ion conditioning agents.
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Affiliation(s)
- Wei Pan
- Department of Cardiology, the Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhenGuangdongChina,Joint Laboratory of Guangdong‐Hong Kong‐Macao Universities for Nutritional Metabolism and Precise Prevention and Control of Major Chronic DiseaseSun Yat‐sen UniversityShenzhenGuangdongChina
| | - Wei Jie
- Department of Cardiology, the Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhenGuangdongChina,Joint Laboratory of Guangdong‐Hong Kong‐Macao Universities for Nutritional Metabolism and Precise Prevention and Control of Major Chronic DiseaseSun Yat‐sen UniversityShenzhenGuangdongChina
| | - Hui Huang
- Department of Cardiology, the Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhenGuangdongChina,Joint Laboratory of Guangdong‐Hong Kong‐Macao Universities for Nutritional Metabolism and Precise Prevention and Control of Major Chronic DiseaseSun Yat‐sen UniversityShenzhenGuangdongChina
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11
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Tian Y, Fu S, Zhang N, Zhang H, Li L. The abdominal aortic aneurysm-related disease model based on machine learning predicts immunity and m1A/m5C/m6A/m7G epigenetic regulation. Front Genet 2023; 14:1131957. [PMID: 36911406 PMCID: PMC9995589 DOI: 10.3389/fgene.2023.1131957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 02/13/2023] [Indexed: 02/25/2023] Open
Abstract
Introduction: Abdominal aortic aneurysms (AAA) are among the most lethal non-cancerous diseases. A comprehensive analysis of the AAA-related disease model has yet to be conducted. Methods: Weighted correlation network analysis (WGCNA) was performed for the AAA-related genes. Machine learning random forest and LASSO regression analysis were performed to develop the AAA-related score. Immune characteristics and epigenetic characteristics of the AAA-related score were explored. Results: Our study developed a reliable AAA-related disease model for predicting immunity and m1A/m5C/m6A/m7G epigenetic regulation. Discussion: The pathogenic roles of four model genes, UBE2K, TMEM230, VAMP7, and PUM2, in AAA, need further validation by in vitro and in vivo experiments.
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Affiliation(s)
- Yu Tian
- Department of Vascular Surgery, The Second Hospital of Dalian Medical University, Dalian, China
| | - Shengjie Fu
- Department of Vascular Surgery, The Second Hospital of Dalian Medical University, Dalian, China
| | - Nan Zhang
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | - Hao Zhang
- Department of Neurosurgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Lei Li
- Department of Vascular Surgery, The Second Hospital of Dalian Medical University, Dalian, China
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12
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Zheng H, Hua J, Li H, He W, Chen X, Ji Y, Li Q. Comprehensive analysis of the expression of N6-methyladenosine RNA methylation regulators in pulmonary artery hypertension. Front Genet 2022; 13:974740. [PMID: 36171892 PMCID: PMC9510777 DOI: 10.3389/fgene.2022.974740] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/11/2022] [Indexed: 11/19/2022] Open
Abstract
Background: Pulmonary arterial hypertension (PAH) is a progressive disease characterized by pulmonary vascular remodeling. The development of PAH involves N6-methyladenosine (m6A) modification. However, the functional role of m6A regulators in PAH and the underlying regulatory mechanisms remain unknown so far. Methods: Microarray data (GSE149713) for monocrotaline induced PAH (MCT-PAH) rat models were downloaded and screened for differentially expressed genes (DEGs) and m6A regulators. Next, we screened for differentially expressed m6A regulators in endothelial cells (ECs), smooth muscle cells (SMCs), fibroblasts, interstitial macrophages, NK cells, B cells, T cells, regulatory T cells (Tregs) using scRNA sequencing data. The target DEGs of m6A regulators in ECs, SMCs, fibroblasts, and Tregs were functionally annotated using the Gene Ontology (GO) functional analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. In addition, the cellular interaction analysis was performed to reveal the receptor—ligand pairs regulated by m6A regulators. Pseudo-time trajectory analyses were performed and a ceRNA network of lncRNAs-miRNAs-mRNAs was constructed in SMCs. Furthermore, the RNA transcriptome sequencing data for the SMCs isolated from idiopathic PAH (IPAH) patients (GSE144274) were validated for differentially expressed m6A regulators. Moreover, the HNRNPA2B1 levels in the lung samples from PAH patients and MCT-PAH were determined using immunohistochemistry. Results: The m6A regulators were observed to be dysregulated in PAH. HNRNPA2B1expression level was increased in the PASMCs of scRNAs and IPAH patients. The target DEGs of HNRNPA2B1 were enriched in the regulation of muscle cell differentiation and vasculature development in PASMCs. The HNRNPA2B1 expression levels determined were consistent with the proliferation-related and collagen synthesis-related gene COL4A1. Moreover, the predicted transcription factors (TFs) foxd2/3 and NFκB could be involved in the regulation of HNRNPA2B1. HNRNPA2B1 might be regulating SMCs proliferation and phenotypic transition via rno-miR-330–3p/TGFβR3 and rno-miR-125a-3p/slc39a1. In addition, HNRNPA2B1 was observed to be highly expressed in the lung samples from MCT-PAH rat models and patients with PAH. Conclusion: In summary, the present study identified certain key functional m6A regulators that are involved in pulmonary vascular remodeling. The investigation of m6A patterns might be promising and provide biomarkers for diagnosis and treatment of PAH in the future.
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Affiliation(s)
| | | | | | | | | | - Yingqun Ji
- *Correspondence: Yingqun Ji, ; Qiang Li,
| | - Qiang Li
- *Correspondence: Yingqun Ji, ; Qiang Li,
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13
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Abstract
Unveiling the secrets of genome’s flexibility does not only foster new research in the field, but also gives rise to the exploration and development of novel epigenetic-based therapies as an approach to alleviate disease phenotypes. A better understanding of chromatin biology (DNA/histone complexes) and non-coding RNAs (ncRNAs) has enabled the development of epigenetic drugs able to modulate transcriptional programs implicated in cardiovascular diseases. This particularly applies to heart failure, where epigenetic networks have shown to underpin several pathological features, such as left ventricular hypertrophy, fibrosis, cardiomyocyte apoptosis and microvascular dysfunction. Targeting epigenetic signals might represent a promising approach, especially in patients with heart failure with preserved ejection fraction (HFpEF), where prognosis remains poor and breakthrough therapies have yet to be approved. In this setting, epigenetics can be employed for the development of customized therapeutic approaches thus paving the way for personalized medicine. Even though the beneficial effects of epi-drugs are gaining attention, the number of epigenetic compounds used in the clinical practice remains low suggesting that more selective epi-drugs are needed. From DNA-methylation changes to non-coding RNAs, we can establish brand-new regulations for drug targets with the aim of restoring healthy epigenomes and transcriptional programs in the failing heart. In the present review, we bring the timeline of epi-drug discovery and development, thus highlighting the emerging role of epigenetic therapies in heart failure.
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Affiliation(s)
- Era Gorica
- Center for Molecular Cardiology, University of Zürich, Schlieren, Switzerland.,Department of Pharmacy, University of Pisa, Pisa, Italy
| | - Shafeeq A Mohammed
- Center for Molecular Cardiology, University of Zürich, Schlieren, Switzerland
| | - Samuele Ambrosini
- Center for Molecular Cardiology, University of Zürich, Schlieren, Switzerland
| | | | - Sarah Costantino
- Center for Molecular Cardiology, University of Zürich, Schlieren, Switzerland.,Department of Cardiology, University Heart Center, Zurich, Switzerland
| | - Francesco Paneni
- Center for Molecular Cardiology, University of Zürich, Schlieren, Switzerland.,Department of Cardiology, University Heart Center, Zurich, Switzerland.,Department of Research and Education, University Hospital Zurich, Zurich, Switzerland
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Vausort M, Niedolistek M, Lumley AI, Oknińska M, Paterek A, Mączewski M, Dong X, Jäger C, Linster CL, Leszek P, Devaux Y. Regulation of N6-Methyladenosine after Myocardial Infarction. Cells 2022; 11:2271. [PMID: 35892568 PMCID: PMC9329994 DOI: 10.3390/cells11152271] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 07/19/2022] [Accepted: 07/19/2022] [Indexed: 12/10/2022] Open
Abstract
Development of heart failure (HF) after myocardial infarction (MI) is responsible for premature death. Complex cellular and molecular mechanisms are involved in this process. A number of studies have linked the epitranscriptomic RNA modification N6-methyladenosine (m6A) with HF, but it remains unknown how m6A affects the risk of developing HF after MI. We addressed the regulation of m6A and its demethylase fat mass and obesity-associated (FTO) after MI and their association with HF. Using liquid chromatography coupled to mass spectrometry, we observed an increase of m6A content in the infarcted area of rat hearts subjected to coronary ligation and a decrease in blood. FTO expression measured by quantitative PCR was downregulated in the infarcted hearts. In whole blood samples collected at the time of reperfusion in MI patients, m6A content was lower in patients who developed HF as attested by a 4-month ejection fraction (EF) of ≤40% as compared to patients who did not develop HF (EF > 50%). M6A content was higher in females. These results show that m6A measured in blood is associated with HF development after MI and motivate further investigation of the potential role of m6A as a novel epitranscriptomics biomarker and therapeutic target of HF.
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He C, Zhu X, Kong F, Zhang X, Chai X, Zou C, Zhao D. The Value of m5C-Related lncRNAs in the Prognostic Assessment and Immunotherapy of Stomach Adenocarcinoma. Biomed Res Int 2022; 2022:2747799. [PMID: 35711526 DOI: 10.1155/2022/2747799] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/24/2022] [Indexed: 12/16/2022]
Abstract
Long noncoding RNAs (lncRNAs) are closely associated with a variety of tumors, including stomach adenocarcinoma (STAD). However, the role of 5-methylcytosine- (m5C-) related lncRNAs in STAD is still uncertain. This study investigated the value of m5C-related lncRNAs in prognostic evaluation and immunotherapy of STAD. STAD transcriptome sequencing data were downloaded from The Cancer Genome Atlas (TCGA) database, and m5C-related lncRNAs were screened by Pearson correlation analysis. A prognostic m5C-related lncRNA signature (m5CRLSig) associated with STAD was established using univariate and multivariate Cox regression analysis. We constructed a prognostic risk model for STAD with six m5C-related lncRNAs. The receiver operating characteristic (ROC) curve was used to examine the predictive efficacy. Univariate and multifactorial Cox regression analysis and principal component analysis (PCA) validated m5CRLSig as an independent factor of STAD prognosis. The clinicopathological characteristics of the model showed higher risk scores for stages II-IV, grade 3, N1-3, and death status. The calibration curve of a nomogram revealed that the nomogram had an excellent predictive function for survival risk. Furthermore, the expression of six m5C-related lncRNAs in STAD and paracancerous tissues was detected by quantitative real-time PCR (qRT-PCR), which verified the feasibility of the m5CRLSig as a prognostic marker for STAD. m5C-related lncRNAs were linked to multiple immune-associated pathways, according to gene set enrichment analysis (GSEA). CIBERSORT analysis indicated that m5CRLSig was involved in immune cell infiltration. Risk score was associated with immune checkpoint gene expression, immune function scores, and chemotherapeutic drug sensitivity. Therefore, m5CRLSig can efficiently assess the prognosis of STAD patients and can be used as a biological marker for immunotherapy.
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Wu Y, Jiang D, Zhang H, Yin F, Guo P, Zhang X, Bian C, Chen C, Li S, Yin Y, Böckler D, Zhang J, Han Y. N1-Methyladenosine (m1A) Regulation Associated With the Pathogenesis of Abdominal Aortic Aneurysm Through YTHDF3 Modulating Macrophage Polarization. Front Cardiovasc Med 2022; 9:883155. [PMID: 35620523 PMCID: PMC9127271 DOI: 10.3389/fcvm.2022.883155] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/20/2022] [Indexed: 11/30/2022] Open
Abstract
Objectives This study aimed to identify key AAA-related m1A RNA methylation regulators and their association with immune infiltration in AAA. Furthermore, we aimed to explore the mechanism that m1A regulators modulate the functions of certain immune cells as well as the downstream target genes, participating in the progression of AAA. Methods Based on the gene expression profiles of the GSE47472 and GSE98278 datasets, differential expression analysis focusing on m1A regulators was performed on the combined dataset to identify differentially expressed m1A regulatory genes (DEMRGs). Additionally, CIBERSORT tool was utilized in the analysis of the immune infiltration landscape and its correlation with DEMRGs. Moreover, we validated the expression levels of DEMRGs in human AAA tissues by real-time quantitative PCR (RT-qPCR). Immunofluorescence (IF) staining was also applied in the validation of cellular localization of YTHDF3 in AAA tissues. Furthermore, we established LPS/IFN-γ induced M1 macrophages and ythdf3 knockdown macrophages in vitro, to explore the relationship between YTHDF3 and macrophage polarization. At last, RNA immunoprecipitation-sequencing (RIP-Seq) combined with PPI network analysis was used to predict the target genes of YTHDF3 in AAA progression. Results Eight DEMRGs were identified in our study, including YTHDC1, YTHDF1-3, RRP8, TRMT61A as up-regulated genes and FTO, ALKBH1 as down-regulated genes. The immune infiltration analysis showed these DEMRGs were positively correlated with activated mast cells, plasma cells and M1 macrophages in AAA. RT-qPCR analysis also verified the up-regulated expression levels of YTHDC1, YTHDF1, and YTHDF3 in human AAA tissues. Besides, IF staining result in AAA adventitia indicated the localization of YTHDF3 in macrophages. Moreover, our in-vitro experiments found that the knockdown of ythdf3 in M0 macrophages inhibits macrophage M1 polarization but promotes macrophage M2 polarization. Eventually, 30 key AAA-related target genes of YTHDF3 were predicted, including CD44, mTOR, ITGB1, STAT3, etc. Conclusion Our study reveals that m1A regulation is significantly associated with the pathogenesis of human AAA. The m1A “reader,” YTHDF3, may participate in the modulating of macrophage polarization that promotes aortic inflammation, and influence AAA progression by regulating the expression of its target genes.
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Affiliation(s)
- Yihao Wu
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Deying Jiang
- Department of Vascular Surgery, Dalian Municipal Central Hospital, Dalian, China
| | - Hao Zhang
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Fanxing Yin
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Panpan Guo
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Xiaoxu Zhang
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Ce Bian
- Department of Cardiovascular Surgery, The General Hospital of the PLA Rocket Force, Beijing, China
| | - Chen Chen
- School of Biomedical Sciences, University of Queensland, St Lucia, Brisbane, QLD, Australia
| | - Shuixin Li
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Yuhan Yin
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Dittmar Böckler
- Department of Vascular and Endovascular Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Jian Zhang
- Department of Vascular Surgery, The First Hospital of China Medical University, Shenyang, China
- *Correspondence: Jian Zhang
| | - Yanshuo Han
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
- Yanshuo Han ; orcid.org/0000-0002-4897-2998
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Liu M, Xu K, Saaoud F, Shao Y, Zhang R, Lu Y, Sun Y, Drummer C 4th, Li L, Wu S, Kunapuli SP, Criner GJ, Sun J, Shan H, Jiang X, Wang H, Yang X. 29 m(6)A-RNA Methylation (Epitranscriptomic) Regulators Are Regulated in 41 Diseases including Atherosclerosis and Tumors Potentially via ROS Regulation - 102 Transcriptomic Dataset Analyses. J Immunol Res 2022; 2022:1433323. [PMID: 35211628 DOI: 10.1155/2022/1433323] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/31/2021] [Indexed: 12/12/2022] Open
Abstract
We performed a database mining on 102 transcriptomic datasets for the expressions of 29 m6A-RNA methylation (epitranscriptomic) regulators (m6A-RMRs) in 41 diseases and cancers and made significant findings: (1) a few m6A-RMRs were upregulated; and most m6A-RMRs were downregulated in sepsis, acute respiratory distress syndrome, shock, and trauma; (2) half of 29 m6A-RMRs were downregulated in atherosclerosis; (3) inflammatory bowel disease and rheumatoid arthritis modulated m6A-RMRs more than lupus and psoriasis; (4) some organ failures shared eight upregulated m6A-RMRs; end-stage renal failure (ESRF) downregulated 85% of m6A-RMRs; (5) Middle-East respiratory syndrome coronavirus infections modulated m6A-RMRs the most among viral infections; (6) proinflammatory oxPAPC modulated m6A-RMRs more than DAMP stimulation including LPS and oxLDL; (7) upregulated m6A-RMRs were more than downregulated m6A-RMRs in cancer types; five types of cancers upregulated ≥10 m6A-RMRs; (8) proinflammatory M1 macrophages upregulated seven m6A-RMRs; (9) 86% of m6A-RMRs were differentially expressed in the six clusters of CD4+Foxp3+ immunosuppressive Treg, and 8 out of 12 Treg signatures regulated m6A-RMRs; (10) immune checkpoint receptors TIM3, TIGIT, PD-L2, and CTLA4 modulated m6A-RMRs, and inhibition of CD40 upregulated m6A-RMRs; (11) cytokines and interferons modulated m6A-RMRs; (12) NF-κB and JAK/STAT pathways upregulated more than downregulated m6A-RMRs whereas TP53, PTEN, and APC did the opposite; (13) methionine-homocysteine-methyl cycle enzyme Mthfd1 downregulated more than upregulated m6A-RMRs; (14) m6A writer RBM15 and one m6A eraser FTO, H3K4 methyltransferase MLL1, and DNA methyltransferase, DNMT1, regulated m6A-RMRs; and (15) 40 out of 165 ROS regulators were modulated by m6A eraser FTO and two m6A writers METTL3 and WTAP. Our findings shed new light on the functions of upregulated m6A-RMRs in 41 diseases and cancers, nine cellular and molecular mechanisms, novel therapeutic targets for inflammatory disorders, metabolic cardiovascular diseases, autoimmune diseases, organ failures, and cancers.
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Abstract
Diabetes mellitus (DM) and its related complications are among the leading causes of disability and mortality worldwide. Substantial studies have explored epigenetic regulation that is involved in the modifications of DNA and proteins, but RNA modifications in diabetes are still poorly investigated. In recent years, posttranscriptional epigenetic modification of RNA (the so-called 'epitranscriptome') has emerged as an interesting field of research. Numerous modifications, mainly N6 -methyladenosine (m6A), have been identified in nearly all types of RNAs and have been demonstrated to have an indispensable effect in a variety of human diseases, such as cancer, obesity, and diabetes. Therefore, it is particularly important to understand the molecular basis of RNA modifications, which might provide a new perspective for the pathogenesis of diabetes mellitus and the discovery of new therapeutic targets. In this review, we aim to summarize the recent progress in the epitranscriptomics involved in diabetes and diabetes-related complications. We hope to provide some insights for enriching the understanding of the epitranscriptomic regulatory mechanisms of this disease as well as the development of novel therapeutic targets for future clinical benefit.
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Affiliation(s)
- Xinqian Geng
- Department of Endocrinology, The Affiliated Hospital of Yunnan University and the Second People’s Hospital of Yunnan Province, Kunming, China
| | - Zheng Li
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, China
| | - Ying Yang
- Department of Endocrinology, The Affiliated Hospital of Yunnan University and the Second People’s Hospital of Yunnan Province, Kunming, China
- *Correspondence: Ying Yang,
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