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Ding Y, Chen L, Xu J, Feng Y, Liu Q. APAF1 Silencing Ameliorates Diabetic Retinopathy by Suppressing Inflammation, Oxidative Stress, and Caspase-3/GSDME-Dependent Pyroptosis. Diabetes Metab Syndr Obes 2024; 17:1635-1649. [PMID: 38616988 PMCID: PMC11016255 DOI: 10.2147/dmso.s449049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 03/22/2024] [Indexed: 04/16/2024] Open
Abstract
Objective Diabetic retinopathy (DR) can cause permanent blindness with unstated pathogenesis. We aim to find novel biomarkers and explore the mechanism of apoptotic protease activating factor 1 (APAF1) in DR. Methods Differential expression genes (DEGs) were screened based on GSE60436 dataset to find hub genes involved in pyroptosis after comprehensive bioinformatics analysis. DR mice model was constructed by streptozotocin injection. The pathological structure of retina was observed using hematoxylin-eosin staining. The enzyme-linked immunosorbent assay was applied to assess inflammatory factors, vascular endothelial growth factor (VEGF), and oxidative stress. The mRNA and protein expression levels were detected using quantitative real-time polymerase-chain reaction and Western blot. Cell counting kit and flow cytometry were employed to detect proliferation and apoptosis in high glucose-induced ARPE-19 cells. Results Total 71 pyroptosis-related DEGs were screened. BIRC2, CXCL8, APAF1, PPARG, TP53, and CYCS were identified as hub genes of DR. APAF1 was selected as a potential regulator of DR, which was up-regulated in DR mice. APAF1 silencing alleviated retinopathy and inhibited pyroptosis in DR mice with decreased levels of inflammatory factors, VEGF, and oxidative stress. Moreover, APAF1 silencing promoted proliferation while inhibiting apoptosis and caspase-3/GSDME-dependent pyroptosis with a decrease in TNF-α, IL-1β, IL-18, and lactate dehydrogenase in high glucose-induced ARPE-19 cells. Additionally, caspase-3 activator reversed the promotion effect on proliferation and inhibitory effect on apoptosis and pyroptosis after APAF1 silencing in high glucose-induced ARPE-19 cells. Conclusion APAF1 is a novel biomarker for DR and APAF1 silencing inhibits the development of DR by suppressing caspase-3/GSDME-dependent pyroptosis.
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Affiliation(s)
- Yuanyuan Ding
- Department of Ophthalmology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, People’s Republic of China
| | - Linjiang Chen
- Department of Ophthalmology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, People’s Republic of China
| | - Jing Xu
- Department of Ophthalmology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, People’s Republic of China
| | - Yuhan Feng
- Department of Ophthalmology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, People’s Republic of China
| | - Qiong Liu
- Department of Ophthalmology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, People’s Republic of China
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2
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Yang S, Guo X, Cheng W, Seth I, Bulloch G, Chen Y, Shang X, Zhu Z, Huang W, Wang W. Genome-wide DNA methylation analysis of extreme phenotypes in the identification of novel epigenetic modifications in diabetic retinopathy. Clin Epigenetics 2022; 14:137. [PMID: 36316758 PMCID: PMC9623976 DOI: 10.1186/s13148-022-01354-z] [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: 08/21/2022] [Accepted: 10/11/2022] [Indexed: 11/17/2022] Open
Abstract
Background Aberrant epigenetic modifications such as DNA methylation may contribute to the pathogenesis of DR. We aimed at elucidating the role of novel DNA methylation modifications in diabetic retinopathy (DR) in patients with type 2 diabetes mellitus (T2DM) using an extreme phenotypic design. Methods/results Two consecutive studies were conducted. A cross-sectional study using an extreme phenotypic design was conducted to identify rare methylation modifications that might contribute to DR pathogenesis. A 2-year longitudinal nested case–control study was conducted to validate the results and assess whether these novel methylation modifications could be used as biomarkers for predicting DR onset. A large number of differentially methylated CpG sites were identified in the cross-sectional study, and two (cg12869254 and cg04026387) corresponding to known genes were replicated in the longitudinal study. Higher methylation of cg12869254 significantly correlated with macular RNFL thinning in the superior and nasal subregions, and that of cg04026387 correlated with reduced deep capillary plexus VD in the superior and inferior subregions after adjusting for covariates. Conclusions Cg12869254 and cg04026387 hypermethylation may complement the known risk factors that contribute to the pathogenesis of DR and as novel biomarkers for disease prediction. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01354-z.
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Affiliation(s)
- Shaopeng Yang
- grid.12981.330000 0001 2360 039XState Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| | - Xiao Guo
- grid.12981.330000 0001 2360 039XState Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| | - Weijing Cheng
- grid.12981.330000 0001 2360 039XState Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| | - Ishith Seth
- grid.1008.90000 0001 2179 088XCentre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, Level 7, 32 Gisborne Street, East Melbourne, VIC 3002 Australia
| | - Gabriella Bulloch
- grid.1008.90000 0001 2179 088XCentre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, Level 7, 32 Gisborne Street, East Melbourne, VIC 3002 Australia
| | - Yifan Chen
- grid.410556.30000 0001 0440 1440John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Xianwen Shang
- grid.1008.90000 0001 2179 088XCentre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, Level 7, 32 Gisborne Street, East Melbourne, VIC 3002 Australia
| | - Zhuoting Zhu
- grid.1008.90000 0001 2179 088XCentre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, Level 7, 32 Gisborne Street, East Melbourne, VIC 3002 Australia
| | - Wenyong Huang
- grid.12981.330000 0001 2360 039XState Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| | - Wei Wang
- grid.12981.330000 0001 2360 039XState Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
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3
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Hu Q, Zhang X, Sun M, jiang B, Zhang Z, Sun D. Potential epigenetic molecular regulatory networks in ocular neovascularization. Front Genet 2022; 13:970224. [PMID: 36118885 PMCID: PMC9478661 DOI: 10.3389/fgene.2022.970224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/02/2022] [Indexed: 11/23/2022] Open
Abstract
Neovascularization is one of the many manifestations of ocular diseases, including corneal injury and vascular diseases of the retina and choroid. Although anti-VEGF drugs have been used to effectively treat neovascularization, long-term use of anti-angiogenic factors can cause a variety of neurological and developmental side effects. As a result, better drugs to treat ocular neovascularization are urgently required. There is mounting evidence that epigenetic regulation is important in ocular neovascularization. DNA methylation and histone modification, non-coding RNA, and mRNA modification are all examples of epigenetic mechanisms. In order to shed new light on epigenetic therapeutics in ocular neovascularization, this review focuses on recent advances in the epigenetic control of ocular neovascularization as well as discusses these new mechanisms.
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4
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Rajendran S, Seetharaman S, Vetrivel U, Kuppan K. Integrative study of gene expression datasets in retinal samples of Diabetic Retinopathy. Exp Eye Res 2022; 223:109194. [PMID: 35868364 DOI: 10.1016/j.exer.2022.109194] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 06/19/2022] [Accepted: 07/14/2022] [Indexed: 11/16/2022]
Abstract
Diabetic Retinopathy is prevalent among patients with uncontrolled hyperglycemia resulting in vision loss. Despite numerous challenges to create a link among these conditions, the characterization of pathological neovascularization causing retinal damage due to the prognosis of early non-proliferative diabetic retinopathy to late proliferative diabetic retinopathy needs deep understanding. In this study, meta-analysis-based integration of gene expression datasets for the fibrovascular membrane of PDR and neural retina of NPDR were compared, to investigate the differentially expressed genes involved in retinal angiogenesis. Human samples with gene expression profiling of the same experiment type and platform with sufficient information for analysis were included in the study. The studies from cell lines and non-human studies, human samples that include serum, cornea, lens, and/or other ocular tissues or fluids, and studies that lack basic information for analysis were excluded. The microarray datasets available in the Gene Expression Omnibus database of the early and late stages in DR were screened to find common gene expression profiles. Using the INMEX bioinformatics tool, significantly upregulated and downregulated genes in the neural retina of Non-Proliferative Diabetic Retinopathy and fibrovascular membrane of Proliferative Diabetic Retinopathy were compared and studied by the combine effect size method. Using the STRING database PPI network, 50 upregulated and 50 downregulated genes were used to find the key candidate genes involved in retinal disease/degeneration in eye/retinal tissues. In the extensive gene expression meta-analysis performed using INMEX bioinformatics tool, overall, 7935 differentially expressed genes were identified and the respective heatmap was created by using the visualization tools of INVEX. STRING database PPI network identified Retinol Binding Protein 3, Neural Retina Leucine Zipper, S-Antigen Visual Arrestin, Peripherin 2, and Aryl Hydrocarbon Receptor Interacting Protein Like-1 to be the most highly ranked hub genes. The newly discovered potential genes related to retinal angiogenesis causing FVM formation in DR may provide insight into the cellular pathogenesis of NPDR to PDR.
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Affiliation(s)
- Sharmila Rajendran
- Department of Biomedical Sciences, Faculty of Biomedical Sciences, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
| | - Shanmuganathan Seetharaman
- Department of Pharmaceutics, Faculty of Pharmacy, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
| | - Umashankar Vetrivel
- Scientist E, Indian Council of Medical Research (ICMR), National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - Kaviarasan Kuppan
- Department of Biomedical Sciences, Faculty of Biomedical Sciences, Sri Ramachandra Institute of Higher Education and Research, Chennai, India.
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Hellbach F, Baumeister SE, Wilson R, Wawro N, Dahal C, Freuer D, Hauner H, Peters A, Winkelmann J, Schwettmann L, Rathmann W, Kronenberg F, Koenig W, Meisinger C, Waldenberger M, Linseisen J. Association between Usual Dietary Intake of Food Groups and DNA Methylation and Effect Modification by Metabotype in the KORA FF4 Cohort. Life (Basel) 2022; 12:life12071064. [PMID: 35888152 PMCID: PMC9318948 DOI: 10.3390/life12071064] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 11/17/2022] Open
Abstract
Associations between diet and DNA methylation may vary among subjects with different metabolic states, which can be captured by clustering populations in metabolically homogenous subgroups, called metabotypes. Our aim was to examine the relationship between habitual consumption of various food groups and DNA methylation as well as to test for effect modification by metabotype. A cross-sectional analysis of participants (median age 58 years) of the population-based prospective KORA FF4 study, habitual dietary intake was modeled based on repeated 24-h diet recalls and a food frequency questionnaire. DNA methylation was measured using the Infinium MethylationEPIC BeadChip providing data on >850,000 sites in this epigenome-wide association study (EWAS). Three metabotype clusters were identified using four standard clinical parameters and BMI. Regression models were used to associate diet and DNA methylation, and to test for effect modification. Few significant signals were identified in the basic analysis while many significant signals were observed in models including food group-metabotype interaction terms. Most findings refer to interactions of food intake with metabotype 3, which is the metabotype with the most unfavorable metabolic profile. This research highlights the importance of the metabolic characteristics of subjects when identifying associations between diet and white blood cell DNA methylation in EWAS.
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Affiliation(s)
- Fabian Hellbach
- Institute for Medical Information Processing, Biometry and Epidemiology, Medical Faculty, Ludwig-Maximilian University of Munich, Marchioninistr. 15, 81377 Munich, Germany; (N.W.); (J.L.)
- Epidemiology, Faculty of Medicine, University Hospital Augsburg, University of Augsburg, Stenglinstraße 2, 86156 Augsburg, Germany; (C.D.); (D.F.); (C.M.)
- Correspondence: ; Tel.: +49-821-598-6473
| | - Sebastian-Edgar Baumeister
- Institute of Health Services Research in Dentistry, Medical Faculty, University of Münster, Albert-Schweitzer-Campus 1, 48149 Münster, Germany;
| | - Rory Wilson
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; (R.W.); (A.P.); (M.W.)
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Nina Wawro
- Institute for Medical Information Processing, Biometry and Epidemiology, Medical Faculty, Ludwig-Maximilian University of Munich, Marchioninistr. 15, 81377 Munich, Germany; (N.W.); (J.L.)
- Epidemiology, Faculty of Medicine, University Hospital Augsburg, University of Augsburg, Stenglinstraße 2, 86156 Augsburg, Germany; (C.D.); (D.F.); (C.M.)
| | - Chetana Dahal
- Epidemiology, Faculty of Medicine, University Hospital Augsburg, University of Augsburg, Stenglinstraße 2, 86156 Augsburg, Germany; (C.D.); (D.F.); (C.M.)
| | - Dennis Freuer
- Epidemiology, Faculty of Medicine, University Hospital Augsburg, University of Augsburg, Stenglinstraße 2, 86156 Augsburg, Germany; (C.D.); (D.F.); (C.M.)
| | - Hans Hauner
- Else Kröner-Fresenius-Center for Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany;
- Institute of Nutritional Medicine, School of Medicine, Technical University of Munich, Georg-Brauchle-Ring 62, 80992 Munich, Germany
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; (R.W.); (A.P.); (M.W.)
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD e.V.), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
- Institute for Biometrics and Epidemiology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Auf’m Hennekamp 65, 40225 Düsseldorf, Germany;
| | - Juliane Winkelmann
- Institute of Neurogenomic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany;
| | - Lars Schwettmann
- Institute of Health Economics and Health Care Management, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany;
- Department of Economics, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Wolfgang Rathmann
- Institute for Biometrics and Epidemiology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Auf’m Hennekamp 65, 40225 Düsseldorf, Germany;
| | - Florian Kronenberg
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstr. 41, 6020 Innsbruck, Austria;
| | - Wolfgang Koenig
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Pettenkoferstr. 8A & 9, 80336 Munich, Germany;
- German Heart Centre Munich, Technical University Munich, Lazarettstr. 36, 80636 Munich, Germany
- Institute of Epidemiology and Medical Biometry, University of Ulm, Helmholtzstr. 22, 89081 Ulm, Germany
| | - Christa Meisinger
- Epidemiology, Faculty of Medicine, University Hospital Augsburg, University of Augsburg, Stenglinstraße 2, 86156 Augsburg, Germany; (C.D.); (D.F.); (C.M.)
| | - Melanie Waldenberger
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; (R.W.); (A.P.); (M.W.)
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
- Institute for Biometrics and Epidemiology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Auf’m Hennekamp 65, 40225 Düsseldorf, Germany;
| | - Jakob Linseisen
- Institute for Medical Information Processing, Biometry and Epidemiology, Medical Faculty, Ludwig-Maximilian University of Munich, Marchioninistr. 15, 81377 Munich, Germany; (N.W.); (J.L.)
- Epidemiology, Faculty of Medicine, University Hospital Augsburg, University of Augsburg, Stenglinstraße 2, 86156 Augsburg, Germany; (C.D.); (D.F.); (C.M.)
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6
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Barnstable CJ. Epigenetics and Degenerative Retinal Diseases: Prospects for New Therapeutic Approaches. Asia Pac J Ophthalmol (Phila) 2022; 11:328-334. [PMID: 36041147 DOI: 10.1097/apo.0000000000000520] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/08/2022] [Indexed: 12/26/2022] Open
Abstract
ABSTRACT There is growing evidence that retinal degenerative diseases are accompanied by epigenetic changes in both deoxyribonucleic acid methylation and histone modification. Even in the monogenic disease retinitis pigmentosa, there is a cascade of changes in gene expression that correlate with epigenetic changes, suggesting that many of the symptoms, and degenerative changes, may be a result of epigenetic changes downstream from the genetic mutation. This is supported by data from studies of diabetic retinopathy and macular degeneration, 2 diseases where it has been difficult to define a single causative change. Initial studies with modifiers of deoxyribonucleic acid methylation suggest that they can provide therapeutic benefit. A number of drugs are available to inhibit specific epigenetic histone modifier enzymes, and these offer the possibility of new therapeutic approaches to retinal disease. Systemic treatment with inhibitors of histone demethylases and histone deacetylases have arrested rod degeneration in rodent models of retinitis pigmentosa. Some evidence has suggested that similar treatments may provide benefits for patients with diabetic retinopathy. Because differentiation of retinal stem cells is regulated in part by epigenetic mechanisms, it may also be possible to direct stem cell differentiation pathways through the use of selective epigenetic modifiers. This is predicted to provide a valuable avenue to accelerate the introduction of regenerative approaches to retinal disease. Epigenetic modifiers are poised to become a powerful new approach to treat retinal degenerative diseases.
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Affiliation(s)
- Colin J Barnstable
- Department of Neural and Behavioral Sciences, Penn State College of Medicine, PA, US
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He C, Wang D, Wang R, Huang Y, Huang X, Shen S, Lv J, Wu M. Epigallocatechin Gallate Induces the Demethylation of Actinin Alpha 4 to Inhibit Diabetic Nephropathy Renal Fibrosis via the NF-KB Signaling Pathway In Vitro. Dose Response 2022; 20:15593258221105704. [PMID: 35706474 PMCID: PMC9189538 DOI: 10.1177/15593258221105704] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 05/10/2022] [Accepted: 05/17/2022] [Indexed: 11/15/2022]
Abstract
Actinin alpha 4 (ACTN4) is expressed in the kidney podocytes. ACTN4 gene methylation in patients with diabetic nephropathy (DN) remains high. Underlying mechanism of epigallocatechin-3-gallate (EGCG) inducing ACTN4 demethylation, and its inhibitory effect on DN renal fibrosis remains unclear.
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Affiliation(s)
- Chunling He
- Department of Endocrinology and Genetic Metabolism, Yijishan Hospital of Wannan Medical College, Wuhu, China
| | - Dong Wang
- Department of Hepatobiliary Surgery, Yijishan Hospital of Wannan Medical College, Wuhu, China
| | - Ruoling Wang
- Department of Biochemistry and Molecular Biology, Wannan Medical College, Wuhu, China
| | - Yongli Huang
- Department of Biochemistry and Molecular Biology, Wannan Medical College, Wuhu, China
| | - Xin Huang
- Department of Biochemistry and Molecular Biology, Wannan Medical College, Wuhu, China
| | - ShuMin Shen
- Department of Biochemistry and Molecular Biology, Wannan Medical College, Wuhu, China
| | - Jun Lv
- Department of Biochemistry and Molecular Biology, Wannan Medical College, Wuhu, China
| | - Mingcai Wu
- Department of Biochemistry and Molecular Biology, Wannan Medical College, Wuhu, China
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8
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Wang N, Ding L, Liu D, Zhang Q, Zheng G, Xia X, Xiong S. Molecular investigation of candidate genes for pyroptosis-induced inflammation in diabetic retinopathy. Front Endocrinol (Lausanne) 2022; 13:918605. [PMID: 35957838 PMCID: PMC9357938 DOI: 10.3389/fendo.2022.918605] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Diabetic retinopathy is a diabetic microvascular complication. Pyroptosis, as a way of inflammatory death, plays an important role in the occurrence and development of diabetic retinopathy, but its underlying mechanism has not been fully elucidated. The purpose of this study is to identify the potential pyroptosis-related genes in diabetic retinopathy by bioinformatics analysis and validation in a diabetic retinopathy model and predict the microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) interacting with them. Subsequently, the competing endogenous RNA (ceRNA) regulatory network is structured to explore their potential molecular mechanism. METHODS We obtained mRNA expression profile dataset GSE60436 from the Gene Expression Omnibus (GEO) database and collected 51 pyroptosis-related genes from the PubMmed database. The differentially expressed pyroptosis-related genes were obtained by bioinformatics analysis with R software, and then eight key genes of interest were identified by correlation analysis, Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and protein-protein interaction (PPI) network analysis. Then, the expression levels of these key pyroptosis-related genes were validated with quantitative real-time polymerase chain reaction (qRT-PCR) in human retinal endothelial cells with high glucose incubation, which was used as an in vitro model of diabetic retinopathy. Western blot was performed to measure the protein levels of gasdermin D (GSDMD), dasdermin E (GSDME) and cleaved caspase-3 in the cells. Moreover, the aforementioned genes were further confirmed with the validation set. Finally, the ceRNA regulatory network was structured, and the miRNAs and lncRNAs which interacted with CASP3, TLR4, and GBP2 were predicted. RESULTS A total of 13 differentially expressed pyroptosis-related genes were screened from six proliferative diabetic retinopathy patients and three RNA samples from human retinas, including one downregulated gene and 12 upregulated genes. A correlation analysis showed that there was a correlation among these genes. Then, KEGG pathway and GO enrichment analyses were performed to explore the functional roles of these genes. The results showed that the mRNA of these genes was mainly related to inflammasome complex, interleukin-1 beta production, and NOD-like receptor signaling pathway. In addition, eight hub genes-CASP3, TLR4, NLRP3, GBP2, CASP1, CASP4, PYCARD, and GBP1-were identified by PPI network analysis using Cytoscape software. High glucose increased the protein level of GSDMD and GSDME, as critical effectors of pyroptosis, in retinal vascular endothelial cells. Verified by qRT-PCR, the expression of all these eight hub genes in the in vitro model of diabetic retinopathy was consistent with the results of the bioinformatics analysis of mRNA chip. Among them, CASP4, GBP1, CASP3, TLR4, and GBP2 were further validated in the GSE179568 dataset. Finally, 20 miRNAs were predicted to target three key genes-CASP3, GBP2, and TLR4, and 22 lncRNAs were predicted to potentially bind to these 20 miRNAs. Then, we constructed a key ceRNA network that is expected to mediate cellular pyroptosis in diabetic retinopathy. CONCLUSION Through the data analysis of the GEO database by R software and verification by qRT-PCR and validation set, we successfully identified potential pyroptosis-related genes involved in the occurrence of diabetic retinopathy. The key ceRNA regulatory network associated with these genes was structured. These findings might improve the understanding of molecular mechanisms underlying pyroptosis in diabetic retinopathy.
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Affiliation(s)
- Nan Wang
- Eye Center of Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Ophthalmology, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Lexi Ding
- Eye Center of Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Ophthalmology, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Die Liu
- Eye Center of Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Ophthalmology, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Quyan Zhang
- Eye Center of Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Ophthalmology, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Guoli Zheng
- Eye Center of Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Ophthalmology, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Xiaobo Xia
- Eye Center of Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Ophthalmology, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Siqi Xiong
- Eye Center of Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Ophthalmology, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Siqi Xiong,
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