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Wang R, Xue W, Kan F, Zhang H, Wang D, Wang L, Wang J. NSUN2 affects diabetic retinopathy progression by regulating MUC1 expression through RNA m 5C methylation. J Transl Med 2024; 22:476. [PMID: 38764010 PMCID: PMC11103891 DOI: 10.1186/s12967-024-05287-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 05/10/2024] [Indexed: 05/21/2024] Open
Abstract
BACKGROUND Diabetic retinopathy (DR) is the leading cause of blinding eye disease among working adults and is primarily attributed to the excessive proliferation of microvessels, which leads to vitreous hemorrhage and retinal traction, thereby significantly impairing patient vision. NSUN2-mediated RNA m5C methylation is implicated in various diseases, and in this investigation, we focused on elucidating the impact of NSUN2 on the regulation of the expression of the downstream gene MUC1, specifically through RNA m5C methylation, on the progression of DR. METHOD Utilizing Microarray analysis, we examined patient vitreous fluid to pinpoint potential therapeutic targets for DR. Differential expression of NSUN2 was validated through qRT-PCR, Western blot, and immunofluorescence in human tissue, animal tissue, and cell model of DR. The relationship between NSUN2 and DR was explored in vitro and in vivo through gene knockdown and overexpression. Various techniques, such as MeRIP-qPCR and dot blot, were applied to reveal the downstream targets and mechanism of action of NSUN2. RESULTS The levels of both NSUN2 and RNA m5C methylation were significantly elevated in the DR model. Knockdown of NSUN2 mitigated DR lesion formation both in vitro and in vivo. Mechanistically, NSUN2 promoted MUC1 expression by binding to the RNA m5C reader ALYREF. Knockdown of ALYREF resulted in DR lesion alterations similar to those observed with NSUN2 knockdown. Moreover, MUC1 overexpression successfully reversed a series of DR alterations induced by NSUN2 silencing. CONCLUSIONS NSUN2 regulates the expression of MUC1 through ALYREF-mediated RNA m5C methylation, thereby regulating the progression of DR and providing a new option for the treatment of DR in the future.
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Affiliation(s)
- Runze Wang
- Eye Hospital, The First Affiliated Hospital of Harbin Medical University, Harbin, 150000, China
| | - Wei Xue
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Feifei Kan
- Eye Hospital, The First Affiliated Hospital of Harbin Medical University, Harbin, 150000, China
| | - Huiying Zhang
- Eye Hospital, The First Affiliated Hospital of Harbin Medical University, Harbin, 150000, China
| | - Di Wang
- Eye Hospital, The First Affiliated Hospital of Harbin Medical University, Harbin, 150000, China
| | - Lei Wang
- Eye Hospital, The First Affiliated Hospital of Harbin Medical University, Harbin, 150000, China.
| | - Jianwen Wang
- Eye Hospital, The First Affiliated Hospital of Harbin Medical University, Harbin, 150000, China.
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Alhammadi MA, Bajbouj K, Talaat IM, Hamoudi R. The role of RNA-modifying proteins in renal cell carcinoma. Cell Death Dis 2024; 15:227. [PMID: 38503745 PMCID: PMC10951318 DOI: 10.1038/s41419-024-06479-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 01/09/2024] [Accepted: 01/17/2024] [Indexed: 03/21/2024]
Abstract
Gene expression is one of the most critical cellular processes. It is controlled by complex mechanisms at the genomic, epigenomic, transcriptomic, and proteomic levels. Any aberration in these mechanisms can lead to dysregulated gene expression. One recently discovered process that controls gene expression includes chemical modifications of RNA molecules by RNA-modifying proteins, a field known as epitranscriptomics. Epitranscriptomics can regulate mRNA splicing, nuclear export, stabilization, translation, or induce degradation of target RNA molecules. Dysregulation in RNA-modifying proteins has been found to contribute to many pathological conditions, such as cancer, diabetes, obesity, cardiovascular diseases, and neurological diseases, among others. This article reviews the role of epitranscriptomics in the pathogenesis and progression of renal cell carcinoma. It summarizes the molecular function of RNA-modifying proteins in the pathogenesis of renal cell carcinoma.
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Affiliation(s)
- Muna A Alhammadi
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates.
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates.
| | - Khuloud Bajbouj
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates.
- Department of Basic Sciences, College of Medicine, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates.
- Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, United States of America.
| | - Iman M Talaat
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates.
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates.
- Pathology Department, Faculty of Medicine, Alexandria University, 21131, Alexandria, Egypt.
| | - Rifat Hamoudi
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates.
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates.
- Division of Surgery and Interventional Science, University College London, London, NW3 2PS, United Kingdom.
- ASPIRE Precision Medicine Research Institute Abu Dhabi, University of Sharjah, Sharjah, United Arab Emirates.
- BIMAI-Lab, Biomedically Informed Artificial Intelligence Laboratory, University of Sharjah, Sharjah, United Arab Emirates.
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Shen J, Chen H, Dai J. Genome-wide screening of m6A profiling of cutaneous wound healing in diabetic mice. Mol Biol Rep 2024; 51:175. [PMID: 38252224 DOI: 10.1007/s11033-023-09089-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 11/29/2023] [Indexed: 01/23/2024]
Abstract
OBJECTIVE Impaired wound healing in diabetes mellitus (DM) is a major health burden on patients, their families, and society. The present study aimed to systematically profile the m6A modification landscape in cutaneous wounds in a diabetic mouse model. APPROACH Diabetes was induced in mice through a single intraperitoneal injection of streptozotocin (STZ); a single intraperitoneal injection of PBS was made in control mice for comparisons. Both groups then received an 8-mm diameter, full-thickness dorsal body wound with a biopsy punch. Five days after wound surgery, western blot analysis of harvested wound tissues from both groups was used to assess the expression of m6A-related enzymes. Genome-wide profiling of m6A-tagged transcripts was performed through MeRIP-seq and RNA-seq. RESULTS ALKBH5, an m6A eraser, was significantly upregulated, while METTL3, METTL14, and WTAP, m6A writers, were markedly downregulated in the diabetic wounds. Additionally, a total of 1335 m6A peaks were differentially expressed in MeRIP-seq and RNA-seq analyses, with 558 upregulated and 777 downregulated peaks. Finally, there was hypomethylated and hypermethylated differentiation at the gene and transcript levels. INNOVATION The present study was the first to reveal the m6A landscape in diabetic wounds in an animal model. CONCLUSION This study, by deeply analyzing the role of m6A modifications in diabetic wound healing, provides new insights and understanding into the molecular mechanisms of diabetic wound healing. Future research could further explore how m6A modifications regulate the wound healing process, thereby offering new potential targets for the treatment of diabetic wounds.
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Affiliation(s)
- Junjie Shen
- Department of Orthopedic Surgery, Shanghai Sixth People's Hospital, JiaoTong University, Shanghai, China
| | - Hua Chen
- Department of Orthopedic Surgery, Shanghai Sixth People's Hospital, JiaoTong University, Shanghai, China.
| | - Jiezhi Dai
- Department of Orthopedic Surgery, Shanghai Sixth People's Hospital, JiaoTong University, Shanghai, China.
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Jazieh C, Arabi TZ, Asim Z, Sabbah BN, Alsaud AW, Alkattan K, Yaqinuddin A. Unraveling the epigenetic fabric of type 2 diabetes mellitus: pathogenic mechanisms and therapeutic implications. Front Endocrinol (Lausanne) 2024; 15:1295967. [PMID: 38323108 PMCID: PMC10845351 DOI: 10.3389/fendo.2024.1295967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/04/2024] [Indexed: 02/08/2024] Open
Abstract
Type 2 diabetes mellitus (T2DM) is a rapidly escalating global health concern, with its prevalence projected to increase significantly in the near future. This review delves into the intricate role of epigenetic modifications - including DNA methylation, histone acetylation, and micro-ribonucleic acid (miRNA) expression - in the pathogenesis and progression of T2DM. We critically examine how these epigenetic changes contribute to the onset and exacerbation of T2DM by influencing key pathogenic processes such as obesity, insulin resistance, β-cell dysfunction, cellular senescence, and mitochondrial dysfunction. Furthermore, we explore the involvement of epigenetic dysregulation in T2DM-associated complications, including diabetic retinopathy, atherosclerosis, neuropathy, and cardiomyopathy. This review highlights recent studies that underscore the diagnostic and therapeutic potential of targeting epigenetic modifications in T2DM. We also provide an overview of the impact of lifestyle factors such as exercise and diet on the epigenetic landscape of T2DM, underscoring their relevance in disease management. Our synthesis of the current literature aims to illuminate the complex epigenetic underpinnings of T2DM, offering insights into novel preventative and therapeutic strategies that could revolutionize its management.
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Quaiyoom A, Kumar R. An Overview of Diabetic Cardiomyopathy. Curr Diabetes Rev 2024; 20:e121023222139. [PMID: 37842898 DOI: 10.2174/0115733998255538231001122639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/13/2023] [Accepted: 08/17/2023] [Indexed: 10/17/2023]
Abstract
Diabetic cardiomyopathy (DCM) is a myocardial disorder that is characterised by structural and functional abnormalities of the heart muscle in the absence of hypertension, valvular heart disease, congenital heart defects, or coronary artery disease (CAD). After witnessing a particular form of cardiomyopathy in diabetic individuals, Rubler et al. came up with the moniker diabetic cardiomyopathy in 1972. Four stages of DCM are documented, and the American College of Cardiology/American Heart Association Stage and New York Heart Association Class for HF have some overlap. Diabetes is linked to several distinct forms of heart failure. Around 40% of people with heart failure with preserved ejection fraction (HFpEF) have diabetes, which is thought to be closely associated with the pathophysiology of HFpEF. Diabetes and HF are uniquely associated in a bidirectional manner. When compared to the general population without diabetes, those with diabetes have a risk of heart failure that is up to four times higher. A biomarker is a trait that is reliably measured and assessed as a predictor of healthy biological activities, pathological processes, or pharmacologic responses to a clinical treatment. Several biomarker values have been discovered to be greater in patients with diabetes than in control subjects among those who have recently developed heart failure. Myocardial fibrosis and hypertrophy are the primary characteristics of DCM, and structural alterations in the diabetic myocardium are often examined by non-invasive, reliable, and reproducible procedures. An invasive method called endomyocardial biopsy (EMB) is most often used to diagnose many cardiac illnesses.
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Affiliation(s)
- Abdul Quaiyoom
- Department of Pharmacy Practice, ISF College of Pharmacy, Moga, India
| | - Ranjeet Kumar
- Department of Pharmacy Practice, ISF College of Pharmacy, Moga, India
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Singh S, Sarma DK, Verma V, Nagpal R, Kumar M. Unveiling the future of metabolic medicine: omics technologies driving personalized solutions for precision treatment of metabolic disorders. Biochem Biophys Res Commun 2023; 682:1-20. [PMID: 37788525 DOI: 10.1016/j.bbrc.2023.09.064] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/13/2023] [Accepted: 09/21/2023] [Indexed: 10/05/2023]
Abstract
Metabolic disorders are increasingly prevalent worldwide, leading to high rates of morbidity and mortality. The variety of metabolic illnesses can be addressed through personalized medicine. The goal of personalized medicine is to give doctors the ability to anticipate the best course of treatment for patients with metabolic problems. By analyzing a patient's metabolomic, proteomic, genetic profile, and clinical data, physicians can identify relevant diagnostic, and predictive biomarkers and develop treatment plans and therapy for acute and chronic metabolic diseases. To achieve this goal, real-time modeling of clinical data and multiple omics is essential to pinpoint underlying biological mechanisms, risk factors, and possibly useful data to promote early diagnosis and prevention of complex diseases. Incorporating cutting-edge technologies like artificial intelligence and machine learning is crucial for consolidating diverse forms of data, examining multiple variables, establishing databases of clinical indicators to aid decision-making, and formulating ethical protocols to address concerns. This review article aims to explore the potential of personalized medicine utilizing omics approaches for the treatment of metabolic disorders. It focuses on the recent advancements in genomics, epigenomics, proteomics, metabolomics, and nutrigenomics, emphasizing their role in revolutionizing personalized medicine.
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Affiliation(s)
- Samradhi Singh
- ICMR- National Institute for Research in Environmental Health, Bhopal Bypass Road, Bhouri, Bhopal, 462030, Madhya Pradesh, India
| | - Devojit Kumar Sarma
- ICMR- National Institute for Research in Environmental Health, Bhopal Bypass Road, Bhouri, Bhopal, 462030, Madhya Pradesh, India
| | - Vinod Verma
- Stem Cell Research Centre, Department of Hematology, Sanjay Gandhi Post-Graduate Institute of Medical Sciences, Lucknow, 226014, Uttar Pradesh, India
| | - Ravinder Nagpal
- Department of Nutrition and Integrative Physiology, College of Health and Human Sciences, Florida State University, Tallahassee, FL, 32306, USA
| | - Manoj Kumar
- ICMR- National Institute for Research in Environmental Health, Bhopal Bypass Road, Bhouri, Bhopal, 462030, Madhya Pradesh, India.
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Camacho P, Ribeiro E, Pereira B, Varandas T, Nascimento J, Henriques J, Dutra-Medeiros M, Delgadinho M, Oliveira K, Silva C, Brito M. DNA methyltransferase expression (DNMT1, DNMT3a and DNMT3b) as a potential biomarker for anti-VEGF diabetic macular edema response. Eur J Ophthalmol 2023; 33:2267-2274. [PMID: 37082811 PMCID: PMC10590013 DOI: 10.1177/11206721231171623] [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] [Received: 10/08/2022] [Accepted: 03/28/2023] [Indexed: 04/22/2023]
Abstract
PURPOSE DNA methylation is involved in Diabetic Retinopathy progression showing a metabolic memory mechanism. However, the association of DNA methyltransferase with diabetic macular edema is still unknown. We aimed to describe the differences in DNA methyltransferase gene expression in patients with different diabetic macular edema responses. METHODS A total of 27 diabetic patients, aged 59-90 years, were prospectively enrolled in this cross-sectional study. The participants were classified into control group (CG, n = 11), diabetic macular edema responders (rDME, n = 9) and non-responder diabetic macular edema (nrDME, n = 7) after anti-vascular endothelial growth factor (anti-VEGF) treatment. Only cases with a complete ophthalmological examination, digital 133° color fundus, and SD-OCT assessments were used. After RNA extraction and first-strand cDNA synthesis, quantitative real-time PCR was performed with specific primers on the CFX Connect™ Real-Time PCR Detection System to assess differential transcriptional expression patterns. RESULTS The DNMT1 gene showed a positive correlation (r = 0.617; p = 0.043) with Best Corrected Visual Acuity (BCVA) in CG, a positive correlation (r = 0.917; p = 0.010) with HbA1c in nrDME and a negative correlation (r = -0.659; p = 0.049) with GCL-IPL thickness in rDME. DNMT3A gene showed a positive correlation (r = -0.890; p = 0.001) with Sub-foveal Choroidal thickness in rDME whereas DNMT3b gene showed a negative correlation (r = -0.815; p = 0.007) with HbA1c and RNFL (r = -0.664; p = 0.026) in CG. CONCLUSIONS Patients with similar metabolic profile risk factors showed associated DNA methyltransferase transcriptional expression patterns differences fitting with the anti-VEGF diabetic macular edema response. Further studies are needed to clarify if these results (1) reflect disease evolution, (2) translate the therapeutic impact, (3) or can help to predict the therapeutic resistance profile.
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Affiliation(s)
- Pedro Camacho
- H&TRC- Health & Technology Research Center, ESTeSL- Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, Lisbon, Portugal
- Ophtalmology Institute Dr. Gama Pinto, Lisbon, Portugal
- iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Edna Ribeiro
- H&TRC- Health & Technology Research Center, ESTeSL- Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, Lisbon, Portugal
| | - Bruno Pereira
- iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Lisbon, Portugal
- Retina Institute of Lisbon, Lisbon, Portugal
| | | | - João Nascimento
- Retina Institute of Lisbon, Lisbon, Portugal
- Beatriz Ângelo Hospital, Lisbon, Portugal
| | | | - Marco Dutra-Medeiros
- iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Lisbon, Portugal
- Central Lisbon Hospital Center, Lisbon, Portugal
| | - Mariana Delgadinho
- H&TRC- Health & Technology Research Center, ESTeSL- Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, Lisbon, Portugal
| | - Ketlyn Oliveira
- H&TRC- Health & Technology Research Center, ESTeSL- Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, Lisbon, Portugal
| | - Carina Silva
- H&TRC- Health & Technology Research Center, ESTeSL- Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, Lisbon, Portugal
| | - Miguel Brito
- H&TRC- Health & Technology Research Center, ESTeSL- Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, Lisbon, Portugal
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Benak D, Benakova S, Plecita-Hlavata L, Hlavackova M. The role of m 6A and m 6Am RNA modifications in the pathogenesis of diabetes mellitus. Front Endocrinol (Lausanne) 2023; 14:1223583. [PMID: 37484960 PMCID: PMC10360938 DOI: 10.3389/fendo.2023.1223583] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/26/2023] [Indexed: 07/25/2023] Open
Abstract
The rapidly developing research field of epitranscriptomics has recently emerged into the spotlight of researchers due to its vast regulatory effects on gene expression and thereby cellular physiology and pathophysiology. N6-methyladenosine (m6A) and N6,2'-O-dimethyladenosine (m6Am) are among the most prevalent and well-characterized modified nucleosides in eukaryotic RNA. Both of these modifications are dynamically regulated by a complex set of epitranscriptomic regulators called writers, readers, and erasers. Altered levels of m6A and also several regulatory proteins were already associated with diabetic tissues. This review summarizes the current knowledge and gaps about m6A and m6Am modifications and their respective regulators in the pathophysiology of diabetes mellitus. It focuses mainly on the more prevalent type 2 diabetes mellitus (T2DM) and its treatment by metformin, the first-line antidiabetic agent. A better understanding of epitranscriptomic modifications in this highly prevalent disease deserves further investigation and might reveal clinically relevant discoveries in the future.
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Affiliation(s)
- Daniel Benak
- Laboratory of Developmental Cardiology, Institute of Physiology of the Czech Academy of Sciences, Prague, Czechia
- Department of Physiology, Faculty of Science, Charles University, Prague, Czechia
| | - Stepanka Benakova
- Laboratory of Pancreatic Islet Research, Institute of Physiology of the Czech Academy of Sciences, Prague, Czechia
- First Faculty of Medicine, Charles University, Prague, Czechia
| | - Lydie Plecita-Hlavata
- Laboratory of Pancreatic Islet Research, Institute of Physiology of the Czech Academy of Sciences, Prague, Czechia
| | - Marketa Hlavackova
- Laboratory of Developmental Cardiology, Institute of Physiology of the Czech Academy of Sciences, Prague, Czechia
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Gómez de Cedrón M, Moreno Palomares R, Ramírez de Molina A. Metabolo-epigenetic interplay provides targeted nutritional interventions in chronic diseases and ageing. Front Oncol 2023; 13:1169168. [PMID: 37404756 PMCID: PMC10315663 DOI: 10.3389/fonc.2023.1169168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 05/24/2023] [Indexed: 07/06/2023] Open
Abstract
Epigenetic modifications are chemical modifications that affect gene expression without altering DNA sequences. In particular, epigenetic chemical modifications can occur on histone proteins -mainly acetylation, methylation-, and on DNA and RNA molecules -mainly methylation-. Additional mechanisms, such as RNA-mediated regulation of gene expression and determinants of the genomic architecture can also affect gene expression. Importantly, depending on the cellular context and environment, epigenetic processes can drive developmental programs as well as functional plasticity. However, misbalanced epigenetic regulation can result in disease, particularly in the context of metabolic diseases, cancer, and ageing. Non-communicable chronic diseases (NCCD) and ageing share common features including altered metabolism, systemic meta-inflammation, dysfunctional immune system responses, and oxidative stress, among others. In this scenario, unbalanced diets, such as high sugar and high saturated fatty acids consumption, together with sedentary habits, are risk factors implicated in the development of NCCD and premature ageing. The nutritional and metabolic status of individuals interact with epigenetics at different levels. Thus, it is crucial to understand how we can modulate epigenetic marks through both lifestyle habits and targeted clinical interventions -including fasting mimicking diets, nutraceuticals, and bioactive compounds- which will contribute to restore the metabolic homeostasis in NCCD. Here, we first describe key metabolites from cellular metabolic pathways used as substrates to "write" the epigenetic marks; and cofactors that modulate the activity of the epigenetic enzymes; then, we briefly show how metabolic and epigenetic imbalances may result in disease; and, finally, we show several examples of nutritional interventions - diet based interventions, bioactive compounds, and nutraceuticals- and exercise to counteract epigenetic alterations.
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Affiliation(s)
- Marta Gómez de Cedrón
- Molecular Oncology Group, IMDEA Food Institute, CEI UAM, CSIC, Madrid, Spain
- Cell Metabolism Unit, IMDEA Food Institute, CEI UAM, CSIC, Madrid, Spain
| | - Rocío Moreno Palomares
- Molecular Oncology Group, IMDEA Food Institute, CEI UAM, CSIC, Madrid, Spain
- FORCHRONIC S.L, Avda. Industria, Madrid, Spain
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Li J, Liu D, Ren J, Li G, Zhao Z, Zhao H, Yan Q, Duan J, Liu Z. Integrated analysis of RNA methylation regulators crosstalk and immune infiltration for predictive and personalized therapy of diabetic nephropathy. Hum Genomics 2023; 17:6. [PMID: 36765416 PMCID: PMC9912588 DOI: 10.1186/s40246-023-00457-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/04/2023] [Indexed: 02/12/2023] Open
Abstract
BACKGROUND RNA methylation is a widely known post-transcriptional regulation which exists in many cancer and immune system diseases. However, the potential role and crosstalk of five types RNA methylation regulators in diabetic nephropathy (DN) and immune microenvironment remain unclear. METHODS The mRNA expression of 37 RNA modification regulators and RNA modification regulators related genes were identified in 112 samples from 5 Gene Expression Omnibus datasets. Nonnegative Matrix Factorization clustering method was performed to determine RNA modification patterns. The ssGSEA algorithms and the expression of human leukocyte antigen were employed to assess the immune microenvironment characteristics. Risk model based on differentially expression genes responsible for the modification regulators was constructed to evaluate its predictive capability in DN patients. Furthermore, the results were validated by using immunofluorescence co-localizations and protein experiments in vitro. RESULTS We found 24 RNA methylation regulators were significant differently expressed in glomeruli in DN group compared with control group. Four methylation-related genes and six RNA regulators were introduced into riskScore model using univariate Logistic regression and integrated LASSO regression, which could precisely distinguish the DN and healthy individuals. Group with high-risk score was associated with high immune infiltration. Three distinct RNA modification patterns were identified, which has significant differences in immune microenvironment, biological pathway and eGFR. Validation analyses showed the METTL3, ADAR1, DNMT1 were upregulated whereas YTHDC1 was downregulated in DN podocyte cell lines comparing with cells cultured by the normal glucose. CONCLUSION Our study reveals that RNA methylation regulators and immune infiltration regulation play critical roles in the pathogenesis of DN. The bioinformatic analyses combine with verification in vitro could provide robust evidence for identification of predictive RNA methylation regulators in DN.
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Affiliation(s)
- Jia Li
- grid.207374.50000 0001 2189 3846Research Institute of Nephrology, Zhengzhou University, Zhengzhou, 450052 People’s Republic of China ,grid.412633.10000 0004 1799 0733Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 People’s Republic of China ,Henan Province Research Center for Kidney Disease, Zhengzhou, 450052 People’s Republic of China ,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, 450052 People’s Republic of China
| | - Dongwei Liu
- grid.207374.50000 0001 2189 3846Research Institute of Nephrology, Zhengzhou University, Zhengzhou, 450052 People’s Republic of China ,grid.412633.10000 0004 1799 0733Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 People’s Republic of China ,Henan Province Research Center for Kidney Disease, Zhengzhou, 450052 People’s Republic of China ,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, 450052 People’s Republic of China
| | - Jingjing Ren
- grid.207374.50000 0001 2189 3846Research Institute of Nephrology, Zhengzhou University, Zhengzhou, 450052 People’s Republic of China ,grid.412633.10000 0004 1799 0733Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 People’s Republic of China ,Henan Province Research Center for Kidney Disease, Zhengzhou, 450052 People’s Republic of China ,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, 450052 People’s Republic of China
| | - Guangpu Li
- grid.207374.50000 0001 2189 3846Research Institute of Nephrology, Zhengzhou University, Zhengzhou, 450052 People’s Republic of China ,grid.412633.10000 0004 1799 0733Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 People’s Republic of China ,Henan Province Research Center for Kidney Disease, Zhengzhou, 450052 People’s Republic of China ,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, 450052 People’s Republic of China
| | - Zihao Zhao
- grid.207374.50000 0001 2189 3846Research Institute of Nephrology, Zhengzhou University, Zhengzhou, 450052 People’s Republic of China ,grid.412633.10000 0004 1799 0733Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 People’s Republic of China ,Henan Province Research Center for Kidney Disease, Zhengzhou, 450052 People’s Republic of China ,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, 450052 People’s Republic of China
| | - Huanhuan Zhao
- grid.207374.50000 0001 2189 3846Research Institute of Nephrology, Zhengzhou University, Zhengzhou, 450052 People’s Republic of China ,grid.412633.10000 0004 1799 0733Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 People’s Republic of China ,Henan Province Research Center for Kidney Disease, Zhengzhou, 450052 People’s Republic of China ,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, 450052 People’s Republic of China
| | - Qianqian Yan
- grid.207374.50000 0001 2189 3846Research Institute of Nephrology, Zhengzhou University, Zhengzhou, 450052 People’s Republic of China ,grid.412633.10000 0004 1799 0733Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 People’s Republic of China ,Henan Province Research Center for Kidney Disease, Zhengzhou, 450052 People’s Republic of China ,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, 450052 People’s Republic of China
| | - Jiayu Duan
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou, 450052, People's Republic of China. .,Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, People's Republic of China. .,Henan Province Research Center for Kidney Disease, Zhengzhou, 450052, People's Republic of China. .,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, 450052, People's Republic of China.
| | - Zhangsuo Liu
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou, 450052, People's Republic of China. .,Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, People's Republic of China. .,Henan Province Research Center for Kidney Disease, Zhengzhou, 450052, People's Republic of China. .,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, 450052, People's Republic of China.
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Zhang W, Zhang S, Dong C, Guo S, Jia W, Jiang Y, Wang C, Zhou M, Gong Y. A bibliometric analysis of RNA methylation in diabetes mellitus and its complications from 2002 to 2022. Front Endocrinol (Lausanne) 2022; 13:997034. [PMID: 36157472 PMCID: PMC9492860 DOI: 10.3389/fendo.2022.997034] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND RNA methylation has emerged as an active research field in diabetes mellitus (DM) and its complications, while few bibliometric analyses have been performed. We aimed to visualize the hotspots and trends using bibliometric analysis to provide a comprehensive and objective overview of the current search state in this field. METHODS The articles and reviews regarding RNA methylation in DM and its complications were from the Web of Science Core Collection. A retrospective bibliometric analysis and science mapping was performed using the CiteSpace software to plot the knowledge maps and predict the hotspots and trends. RESULTS Three hundred seventy-five qualified records were retrieved. The annual publications gradually increased over the past 20 years. These publications mainly came from 66 countries led by Canada and 423 institutions. Leiter and Sievenpiper were the most productive authors, and Jenkins ranked first in the cited authors. Diabetes Care was the most co-cited journal. The most common keywords were "Type 2 diabetes", "cardiovascular disease", "diabetes mellitus", and "n 6 methyladenosine". The extracted keywords mainly clustered in "beta-cell function", "type 2 diabetes", "diabetic nephropathy", "aging", and "n6-methyladenosine". N6-methyladenosine (m6A) in DM and its complications were the developing areas of study. CONCLUSION Studies on RNA methylation, especially m6A modification, are the current hotspots and the future trends in type 2 diabetes (T2D) and diabetic nephropathy (DN), as well as a frontier field for other complications of DM. Strengthening future cooperation and exchange between countries and institutions is strongly advisable to promote research developments in this field.
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Affiliation(s)
- Wenhua Zhang
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Shuwen Zhang
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Chenlu Dong
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Shuaijie Guo
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- Cardiovascular Disease Research Department, Beijing Institute of Chinese Medicine, Beijing, China
| | - Weiyu Jia
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Yijia Jiang
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Churan Wang
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Mingxue Zhou
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- Cardiovascular Disease Research Department, Beijing Institute of Chinese Medicine, Beijing, China
- *Correspondence: Mingxue Zhou, ; Yanbing Gong,
| | - Yanbing Gong
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
- *Correspondence: Mingxue Zhou, ; Yanbing Gong,
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