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Raghubeer S. The influence of epigenetics and inflammation on cardiometabolic risks. Semin Cell Dev Biol 2024; 154:175-184. [PMID: 36804178 DOI: 10.1016/j.semcdb.2023.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 02/13/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023]
Abstract
Cardiometabolic diseases include metabolic syndrome, obesity, type 2 diabetes mellitus, and hypertension. Epigenetic modifications participate in cardiometabolic diseases through several pathways, including inflammation, vascular dysfunction, and insulin resistance. Epigenetic modifications, which encompass alterations to gene expression without mutating the DNA sequence, have gained much attention in recent years, since they have been correlated with cardiometabolic diseases and may be targeted for therapeutic interventions. Epigenetic modifications are greatly influenced by environmental factors, such as diet, physical activity, cigarette smoking, and pollution. Some modifications are heritable, indicating that the biological expression of epigenetic alterations may be observed across generations. Moreover, many patients with cardiometabolic diseases present with chronic inflammation, which can be influenced by environmental and genetic factors. The inflammatory environment worsens the prognosis of cardiometabolic diseases and further induces epigenetic modifications, predisposing patients to the development of other metabolism-associated diseases and complications. A deeper understanding of inflammatory processes and epigenetic modifications in cardiometabolic diseases is necessary to improve our diagnostic capabilities, personalized medicine approaches, and the development of targeted therapeutic interventions. Further understanding may also assist in predicting disease outcomes, especially in children and young adults. This review describes epigenetic modifications and inflammatory processes underlying cardiometabolic diseases, and further discusses advances in the research field with a focus on specific points for interventional therapy.
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Affiliation(s)
- Shanel Raghubeer
- SAMRC/CPUT/Cardiometabolic Health Research Unit, Department of Biomedical Sciences, Faculty of Health & Wellness Sciences, Cape Peninsula University of Technology, South Africa.
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Sagy N, Meyrom N, Beckerman P, Pleniceanu O, Bar DZ. Kidney-specific methylation patterns correlate with kidney function and are lost upon kidney disease progression. Clin Epigenetics 2024; 16:27. [PMID: 38347603 PMCID: PMC10863297 DOI: 10.1186/s13148-024-01642-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 02/07/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Chronological and biological age correlate with DNA methylation levels at specific sites in the genome. Linear combinations of multiple methylation sites, termed epigenetic clocks, can inform us the chronological age and predict multiple health-related outcomes. However, why some sites correlating with lifespan, healthspan, or specific medical conditions remain poorly understood. Kidney fibrosis is the common pathway for chronic kidney disease, which affects 10% of European and US populations. RESULTS Here we identify epigenetic clocks and methylation sites that correlate with kidney function. Moreover, we identify methylation sites that have a unique methylation signature in the kidney. Methylation levels in majority of these sites correlate with kidney state and function. When kidney function deteriorates, all of these sites regress toward the common methylation pattern observed in other tissues. Interestingly, while the majority of sites are less methylated in the kidney and become more methylated with loss of function, a fraction of the sites are highly methylated in the kidney and become less methylated when kidney function declines. These methylation sites are enriched for specific transcription-factor binding sites. In a large subset of sites, changes in methylation patterns are accompanied by changes in gene expression in kidneys of chronic kidney disease patients. CONCLUSIONS These results support the information theory of aging, and the hypothesis that the unique tissue identity, as captured by methylation patterns, is lost as tissue function declines. However, this information loss is not random, but guided toward a baseline that is dependent on the genomic loci. SIGNIFICANCE STATEMENT DNA methylation at specific sites accurately reflects chronological and biological age. We identify sites that have a unique methylation pattern in the kidney. Methylation levels in the majority of these sites correlate with kidney state and function. Moreover, when kidney function deteriorates, all of these sites regress toward the common methylation pattern observed in other tissues. Thus, the unique methylation signature of the kidney is degraded, and epigenetic information is lost, when kidney disease progresses. These methylation sites are enriched for specific and methylation-sensitive transcription-factor binding sites, and associated genes show disease-dependent changes in expression. These results support the information theory of aging, and the hypothesis that the unique tissue identity, as captured by methylation patterns, is lost as tissue function declines.
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Affiliation(s)
- Naor Sagy
- Department of Oral Biology, Goldschleger School of Dental Medicine, The Faculty of Medical and Health Sciences, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Noa Meyrom
- Department of Oral Biology, Goldschleger School of Dental Medicine, The Faculty of Medical and Health Sciences, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Pazit Beckerman
- Kidney Research Lab, The Institute of Nephrology and Hypertension, Sheba Medical Center, Tel-Hashomer and The Faculty of Medical and Health Sciences, Tel-Aviv University, Tel Aviv, Israel
| | - Oren Pleniceanu
- Kidney Research Lab, The Institute of Nephrology and Hypertension, Sheba Medical Center, Tel-Hashomer and The Faculty of Medical and Health Sciences, Tel-Aviv University, Tel Aviv, Israel
| | - Daniel Z Bar
- Department of Oral Biology, Goldschleger School of Dental Medicine, The Faculty of Medical and Health Sciences, Tel Aviv University, 69978, Tel Aviv, Israel.
- The AI and Data Science Center (TAD), Tel Aviv University, 69978, Tel Aviv, Israel.
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Kumar P, Brooks HL. Sex-specific epigenetic programming in renal fibrosis and inflammation. Am J Physiol Renal Physiol 2023; 325:F578-F594. [PMID: 37560775 DOI: 10.1152/ajprenal.00091.2023] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/18/2023] [Accepted: 07/31/2023] [Indexed: 08/11/2023] Open
Abstract
The growing prevalence of hypertension, heart disease, diabetes, and obesity along with an aging population is leading to a higher incidence of renal diseases in society. Chronic kidney disease (CKD) is characterized mainly by persistent inflammation, fibrosis, and gradual loss of renal function leading to renal failure. Sex is a known contributor to the differences in incidence and progression of CKD. Epigenetic programming is an essential regulator of renal physiology and is critically involved in the pathophysiology of renal injury and fibrosis. Epigenetic signaling integrates intrinsic and extrinsic signals onto the genome, and various environmental and hormonal stimuli, including sex hormones, which regulate gene expression and downstream cellular responses. The most extensively studied epigenetic alterations that play a critical role in renal damage include histone modifications and DNA methylation. Notably, these epigenetic alterations are reversible, making them candidates for potential therapeutic targets for the treatment of renal diseases. Here, we will summarize the current knowledge on sex differences in epigenetic modulation of renal fibrosis and inflammation and highlight some possible epigenetic therapeutic strategies for CKD treatment.
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Affiliation(s)
- Prerna Kumar
- Department of Physiology, School of Medicine, Tulane University, New Orleans, Louisiana, United States
| | - Heddwen L Brooks
- Department of Physiology, School of Medicine, Tulane University, New Orleans, Louisiana, United States
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Soltysova A, Begerova P, Jakic K, Kozics K, Sramkova M, Meese E, Smolkova B, Gabelova A. Genome-wide DNA methylome and transcriptome changes induced by inorganic nanoparticles in human kidney cells after chronic exposure. Cell Biol Toxicol 2023; 39:1939-1956. [PMID: 34973136 PMCID: PMC10547624 DOI: 10.1007/s10565-021-09680-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 11/11/2021] [Indexed: 11/02/2022]
Abstract
The unique physicochemical properties make inorganic nanoparticles (INPs) an exciting tool in diagnosis and disease management. However, as INPs are relatively difficult to fully degrade and excrete, their unintended accumulation in the tissue might result in adverse health effects. Herein, we provide a methylome-transcriptome framework for chronic effects of INPs, commonly used in biomedical applications, in human kidney TH-1 cells. Renal clearance is one of the most important routes of nanoparticle excretion; therefore, a detailed evaluation of nanoparticle-mediated nephrotoxicity is an important task. Integrated analysis of methylome and transcriptome changes induced by INPs (PEG-AuNPs, Fe3O4NPs, SiO2NPs, and TiO2NPs) revealed significantly deregulated genes with functional classification in immune response, DNA damage, and cancer-related pathways. Although most deregulated genes were unique to individual INPs, a relatively high proportion of them encoded the transcription factors. Interestingly, FOS hypermethylation inversely correlating with gene expression was associated with all INPs exposures. Our study emphasizes the need for a more comprehensive investigation of INPs' biological safety, especially after chronic exposure.
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Affiliation(s)
- Andrea Soltysova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 841 04, Bratislava, Slovakia
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovakia
| | - Patricia Begerova
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovakia
| | - Kristina Jakic
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovakia
| | - Katarina Kozics
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovakia
| | - Monika Sramkova
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovakia
| | - Eckart Meese
- Institute of Human Genetics, Saarland University, Building 60, 66421, Homburg, Germany
| | - Bozena Smolkova
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovakia
| | - Alena Gabelova
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovakia.
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Nguyen LT, Pollock CA, Saad S. Nutrition and Developmental Origins of Kidney Disease. Nutrients 2023; 15:4207. [PMID: 37836490 PMCID: PMC10574202 DOI: 10.3390/nu15194207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
The developmental programming hypothesis proposes that adverse environmental insults during critical developmental periods increase the risk of diseases later in life. The kidneys are deemed susceptible to such a process, although the exact mechanisms remain elusive. Many factors have been reported to contribute to the developmental origin of chronic kidney diseases (CKD), among which peri-gestational nutrition has a central role, affecting kidney development and metabolism. Physiologically, the link between malnutrition, reduced glomerular numbers, and increased blood pressure is key in the developmental programming of CKD. However, recent studies regarding oxidative stress, mitochondrial dysfunction, epigenetic modifications, and metabolic changes have revealed potential novel pathways for therapeutic intervention. This review will discuss the role of imbalanced nutrition in the development of CKD.
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Affiliation(s)
- Long T. Nguyen
- Renal Research Group, Kolling Institute, St. Leonards, NSW 2065, Australia; (C.A.P.); (S.S.)
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Hill C, Avila-Palencia I, Maxwell AP, Hunter RF, McKnight AJ. Harnessing the Full Potential of Multi-Omic Analyses to Advance the Study and Treatment of Chronic Kidney Disease. FRONTIERS IN NEPHROLOGY 2022; 2:923068. [PMID: 37674991 PMCID: PMC10479694 DOI: 10.3389/fneph.2022.923068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/30/2022] [Indexed: 09/08/2023]
Abstract
Chronic kidney disease (CKD) was the 12th leading cause of death globally in 2017 with the prevalence of CKD estimated at ~9%. Early detection and intervention for CKD may improve patient outcomes, but standard testing approaches even in developed countries do not facilitate identification of patients at high risk of developing CKD, nor those progressing to end-stage kidney disease (ESKD). Recent advances in CKD research are moving towards a more personalised approach for CKD. Heritability for CKD ranges from 30% to 75%, yet identified genetic risk factors account for only a small proportion of the inherited contribution to CKD. More in depth analysis of genomic sequencing data in large cohorts is revealing new genetic risk factors for common diagnoses of CKD and providing novel diagnoses for rare forms of CKD. Multi-omic approaches are now being harnessed to improve our understanding of CKD and explain some of the so-called 'missing heritability'. The most common omic analyses employed for CKD are genomics, epigenomics, transcriptomics, metabolomics, proteomics and phenomics. While each of these omics have been reviewed individually, considering integrated multi-omic analysis offers considerable scope to improve our understanding and treatment of CKD. This narrative review summarises current understanding of multi-omic research alongside recent experimental and analytical approaches, discusses current challenges and future perspectives, and offers new insights for CKD.
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Affiliation(s)
| | | | | | | | - Amy Jayne McKnight
- Centre for Public Health, Queen’s University Belfast, Belfast, United Kingdom
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Witasp A, Luttropp K, Qureshi AR, Barany P, Heimbürger O, Wennberg L, Ekström TJ, Shiels PG, Stenvinkel P, Nordfors L. Longitudinal genome-wide DNA methylation changes in response to kidney failure replacement therapy. Sci Rep 2022; 12:470. [PMID: 35013499 PMCID: PMC8748627 DOI: 10.1038/s41598-021-04321-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 12/13/2021] [Indexed: 01/01/2023] Open
Abstract
Chronic kidney disease (CKD) is an emerging public health priority associated with high mortality rates and demanding treatment regimens, including life-style changes, medications or even dialysis or renal transplantation. Unavoidably, the uremic milieu disturbs homeostatic processes such as DNA methylation and other vital gene regulatory mechanisms. Here, we aimed to investigate how dialysis or kidney transplantation modifies the epigenome-wide methylation signature over 12 months of treatment. We used the Infinium HumanMethylation450 BeadChip on whole blood samples from CKD-patients undergoing either dialysis (n = 11) or kidney transplantation (n = 12) and 24 age- and sex-matched population-based controls. At baseline, comparison between patients and controls identified several significant (PFDR < 0.01) CpG methylation differences in genes with functions relevant to inflammation, cellular ageing and vascular calcification. Following 12 months, the global DNA methylation pattern of patients approached that seen in the control group. Notably, 413 CpG sites remained differentially methylated at follow-up in both treatment groups compared to controls. Together, these data indicate that the uremic milieu drives genome-wide methylation changes that are partially reversed with kidney failure replacement therapy. Differentially methylated CpG sites unaffected by treatment may be of particular interest as they could highlight candidate genes for kidney disease per se.
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Affiliation(s)
- Anna Witasp
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Karolinska University Hospital, M99, 141 86, Stockholm, Sweden
| | - Karin Luttropp
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Abdul Rashid Qureshi
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Karolinska University Hospital, M99, 141 86, Stockholm, Sweden
| | - Peter Barany
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Karolinska University Hospital, M99, 141 86, Stockholm, Sweden
| | - Olof Heimbürger
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Karolinska University Hospital, M99, 141 86, Stockholm, Sweden
| | - Lars Wennberg
- Division of Transplantation Surgery, Department of Clinical Science, Intervention and Technology, Karolinska University Hospital, Stockholm, Sweden
| | - Tomas J Ekström
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Paul G Shiels
- College of Medical, Veterinary and Life Sciences Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Peter Stenvinkel
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Karolinska University Hospital, M99, 141 86, Stockholm, Sweden
| | - Louise Nordfors
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Karolinska University Hospital, M99, 141 86, Stockholm, Sweden.
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Park S, Cho NJ, Heo NH, Rhee EJ, Gil H, Lee EY. Vascular Calcification as a Novel Risk Factor for Kidney Function Deterioration in the Nonelderly. J Am Heart Assoc 2021; 10:e019300. [PMID: 34151587 PMCID: PMC8403323 DOI: 10.1161/jaha.120.019300] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Background The relationship between vascular calcification and chronic kidney disease is well known. However, whether vascular calcification affects renal function deterioration remains unclear. We investigated whether kidney function deteriorated more rapidly in individuals with higher vascular calcification indicated by the coronary artery calcium score (CACS). Methods and Results Individuals with a normal estimated glomerular filtration rate (>60 mL/min per 1.73 m2) who underwent cardiac computed tomography in our institution (a tertiary teaching hospital in Cheonan, Korea) from January 2010 to July 2012 were retrospectively reviewed. All participants were aged 20 to 65 years. Among 739 patients, 447, 175, and 117 had CACSs of 0, 1 to 99, and ≥100 units, respectively. The participants were followed for 7.8 (interquartile range, 5.5–8.8) years. The adjusted annual estimated glomerular filtration rates declined more rapidly in patients in the CACS ≥100 group compared with those in the CACS 0 group (adjusted‐β, −0.40; 95% CI, −0.80 to −0.03) when estimated using a linear mixed model. The adjusted hazard ratio in the CACS ≥100 group for Kidney Disease: Improving Global Outcomes criteria (a drop in estimated glomerular filtration rate category accompanied by a 25% or greater drop in estimated glomerular filtration rate) was 2.52 (1.13–5.61). After propensity score matching, more prevalent renal outcomes (13.2%) were observed in patients with a CACS of ≥100 compared with those with a CACS of 0 (1.9%), with statistical significance (P=0.004). Conclusions Our results showed that renal function declined more rapidly in patients with higher CACSs, suggesting that vascular calcification might be associated with chronic kidney disease progression.
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Affiliation(s)
- Samel Park
- Department of Internal Medicine Soonchunhyang University Cheonan Hospital Cheonan Korea
| | - Nam-Jun Cho
- Department of Internal Medicine Soonchunhyang University Cheonan Hospital Cheonan Korea
| | - Nam Hun Heo
- Department of Biostatistics Soonchunhyang University Cheonan Hospital Cheonan Korea
| | - Eun-Jung Rhee
- Department of Internal Medicine Kangbuk Samsung Hospital Seoul Korea
| | - Hyowook Gil
- Department of Internal Medicine Soonchunhyang University Cheonan Hospital Cheonan Korea
| | - Eun Young Lee
- Department of Internal Medicine Soonchunhyang University Cheonan Hospital Cheonan Korea.,Institute of Tissue Regeneration College of Medicine Soonchunhyang University Cheonan Korea
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