1
|
Pan W, Yun T, Ouyang X, Ruan Z, Zhang T, An Y, Wang R, Zhu P. A blood-based multi-omic landscape for the molecular characterization of kidney stone disease. Mol Omics 2024; 20:322-332. [PMID: 38623715 DOI: 10.1039/d3mo00261f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Kidney stone disease (KSD, also named renal calculi, nephrolithiasis, or urolithiasis) is a common urological disease entailing the formation of minerals and salts that form inside the urinary tract, frequently caused by diabetes, high blood pressure, hypertension, and monogenetic components in most patients. 10% of adults worldwide are affected by KSD, which continues to be highly prevalent and with increasing incidence. For the identification of novel therapeutic targets in KSD, we adopted high-throughput sequencing and mass spectrometry (MS) techniques in this study and carried out an integrative analysis of exosome proteomic data and DNA methylation data from blood samples of normal and KSD individuals. Our research delineated the profiling of exosomal proteins and DNA methylation in both healthy individuals and those afflicted with KSD, finding that the overexpressed proteins and the demethylated genes in KSD samples are associated with immune responses. The consistency of the results in proteomics and epigenetics supports the feasibility of the comprehensive strategy. Our insights into the molecular landscape of KSD pave the way for a deeper understanding of its pathogenic mechanism, providing an opportunity for more precise diagnosis and targeted treatment strategies for KSD.
Collapse
Affiliation(s)
- Weibing Pan
- Department of Urology, Shenzhen Pingshan People's Hospital, Shenzhen, Guangdong 518118, China
| | - Tianwei Yun
- Department of Urology, Shenzhen Pingshan People's Hospital, Shenzhen, Guangdong 518118, China
| | - Xin Ouyang
- Department of Laboratory Medicine, Shenzhen Pingshan People's Hospital, Shenzhen, Guangdong 518118, China.
| | - Zhijun Ruan
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518020, China.
| | - Tuanjie Zhang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518020, China.
| | - Yuhao An
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518020, China.
| | - Rui Wang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518020, China.
| | - Peng Zhu
- Department of Laboratory Medicine, Shenzhen Pingshan People's Hospital, Shenzhen, Guangdong 518118, China.
| |
Collapse
|
2
|
Bravo-Vázquez LA, Paul S, Colín-Jurado MG, Márquez-Gallardo LD, Castañón-Cortés LG, Banerjee A, Pathak S, Duttaroy AK. Exploring the Therapeutic Significance of microRNAs and lncRNAs in Kidney Diseases. Genes (Basel) 2024; 15:123. [PMID: 38275604 PMCID: PMC10815231 DOI: 10.3390/genes15010123] [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: 12/26/2023] [Revised: 01/14/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
MicroRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are two crucial classes of transcripts that belong to the major group of non-coding RNAs (ncRNAs). These RNA molecules have significant influence over diverse molecular processes due to their crucial role as regulators of gene expression. However, the dysregulated expression of these ncRNAs constitutes a fundamental factor in the etiology and progression of a wide variety of multifaceted human diseases, including kidney diseases. In this context, over the past years, compelling evidence has shown that miRNAs and lncRNAs could be prospective targets for the development of next-generation drugs against kidney diseases as they participate in a number of disease-associated processes, such as podocyte and nephron death, renal fibrosis, inflammation, transition from acute kidney injury to chronic kidney disease, renal vascular changes, sepsis, pyroptosis, and apoptosis. Hence, in this current review, we critically analyze the recent findings concerning the therapeutic inferences of miRNAs and lncRNAs in the pathophysiological context of kidney diseases. Additionally, with the aim of driving advances in the formulation of ncRNA-based drugs tailored for the management of kidney diseases, we discuss some of the key challenges and future prospects that should be addressed in forthcoming investigations.
Collapse
Affiliation(s)
- Luis Alberto Bravo-Vázquez
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, Queretaro 76130, Mexico (S.P.)
| | - Sujay Paul
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, Queretaro 76130, Mexico (S.P.)
| | - Miriam Guadalupe Colín-Jurado
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, Queretaro 76130, Mexico (S.P.)
| | - Luis David Márquez-Gallardo
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, Queretaro 76130, Mexico (S.P.)
| | - Luis Germán Castañón-Cortés
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, Queretaro 76130, Mexico (S.P.)
| | - Antara Banerjee
- Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chennai 603103, India
| | - Surajit Pathak
- Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chennai 603103, India
| | - Asim K. Duttaroy
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, N-0316 Oslo, Norway
| |
Collapse
|
3
|
Kim JE, Jo MJ, Cho E, Ahn SY, Kwon YJ, Gim JA, Ko GJ. The Effect of DNA Methylation in the Development and Progression of Chronic Kidney Disease in the General Population: An Epigenome-Wide Association Study Using the Korean Genome and Epidemiology Study Database. Genes (Basel) 2023; 14:1489. [PMID: 37510393 PMCID: PMC10379047 DOI: 10.3390/genes14071489] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND Although knowledge of the genetic factors influencing kidney disease is increasing, epigenetic profiles, which are associated with chronic kidney disease (CKD), have not been fully elucidated. We sought to identify the DNA methylation status of CpG sites associated with reduced kidney function and examine whether the identified CpG sites are associated with CKD development. METHOD We analyzed DNA methylation patterns of 440 participants in the Korean Genome and Epidemiology Study (KoGES) with estimated glomerular filtration rates (eGFRs) ≥ 60 mL/min/1.73 m2 at baseline. CKD development was defined as a decrease in the eGFR of <60 at any time during an 8-year follow-up period ("CKD prediction" analysis). In addition, among the 440 participants, 49 participants who underwent a second methylation profiling were assessed for an association between a decline in kidney function and changes in the degree of methylation of CpG sites during the 8 years ("kidney function slope" analysis). RESULTS In the CKD prediction analysis, methylation profiles of a total of 403,129 CpG sites were evaluated at baseline in 440 participants, and increased and decreased methylation of 268 and 189 CpG sites, respectively, were significantly correlated with the development of CKD in multivariable logistic regression. During kidney function slope analysis using follow-up methylation profiles of 49 participants, the percent methylation changes in 913 CpG sites showed a linear relationship with the percent change in eGFR during 8 years. During functional enrichment analyses for significant CpG sites found in the CKD prediction and kidney function slope analyses, we found that those CpG sites represented MAPK, PI3K/Akt, and Rap1 pathways. In addition, three CpG sites from three genes, NPHS2, CHCHD4, and AHR, were found to be significant in the CKD prediction analysis and related to a decline in kidney function. CONCLUSION It is suggested that DNA methylation on specific genes is associated with the development of CKD and the deterioration of kidney function.
Collapse
Affiliation(s)
- Ji-Eun Kim
- Department of Internal Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
| | - Min-Jee Jo
- Department of Internal Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
| | - Eunjung Cho
- Department of Internal Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
| | - Shin-Young Ahn
- Department of Internal Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
| | - Young-Joo Kwon
- Department of Internal Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
| | - Jeong-An Gim
- Medical Science Research Center, Korea University College of Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
| | - Gang-Jee Ko
- Department of Internal Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
| |
Collapse
|
4
|
Qu L, Jiao B. The Interplay between Immune and Metabolic Pathways in Kidney Disease. Cells 2023; 12:1584. [PMID: 37371054 DOI: 10.3390/cells12121584] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Kidney disease is a significant health problem worldwide, affecting an estimated 10% of the global population. Kidney disease encompasses a diverse group of disorders that vary in their underlying pathophysiology, clinical presentation, and outcomes. These disorders include acute kidney injury (AKI), chronic kidney disease (CKD), glomerulonephritis, nephrotic syndrome, polycystic kidney disease, diabetic kidney disease, and many others. Despite their distinct etiologies, these disorders share a common feature of immune system dysregulation and metabolic disturbances. The immune system and metabolic pathways are intimately connected and interact to modulate the pathogenesis of kidney diseases. The dysregulation of immune responses in kidney diseases includes a complex interplay between various immune cell types, including resident and infiltrating immune cells, cytokines, chemokines, and complement factors. These immune factors can trigger and perpetuate kidney inflammation, causing renal tissue injury and progressive fibrosis. In addition, metabolic pathways play critical roles in the pathogenesis of kidney diseases, including glucose and lipid metabolism, oxidative stress, mitochondrial dysfunction, and altered nutrient sensing. Dysregulation of these metabolic pathways contributes to the progression of kidney disease by inducing renal tubular injury, apoptosis, and fibrosis. Recent studies have provided insights into the intricate interplay between immune and metabolic pathways in kidney diseases, revealing novel therapeutic targets for the prevention and treatment of kidney diseases. Potential therapeutic strategies include modulating immune responses through targeting key immune factors or inhibiting pro-inflammatory signaling pathways, improving mitochondrial function, and targeting nutrient-sensing pathways, such as mTOR, AMPK, and SIRT1. This review highlights the importance of the interplay between immune and metabolic pathways in kidney diseases and the potential therapeutic implications of targeting these pathways.
Collapse
Affiliation(s)
- Lili Qu
- Division of Nephrology, Department of Medicine, School of Medicine, University of Connecticut Health Center, Farmington, CT 06030-1405, USA
| | - Baihai Jiao
- Department of Immunology, School of Medicine, University of Connecticut Health Center, Farmington, CT 06030-1405, USA
| |
Collapse
|
5
|
Xiao X, Huo E, Guo C, Zhou X, Hu X, Dong C, Shi H, Dong Z, Wei Q. Hypermethylation suppresses microRNA-219a-2 to activate the ALDH1L2/GSH/PAI-1 pathway for fibronectin degradation in renal fibrosis. RESEARCH SQUARE 2023:rs.3.rs-2986934. [PMID: 37333081 PMCID: PMC10275039 DOI: 10.21203/rs.3.rs-2986934/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Epigenetic regulations, such as DNA methylation and microRNAs, play an important role in renal fibrosis. Here, we report the regulation of microRNA-219a-2 (mir-219a-2) by DNA methylation in fibrotic kidneys, unveiling the crosstalk between these epigenetic mechanisms. Through genome-wide DNA methylation analysis and pyro-sequencing, we detected the hypermethylation of mir-219a-2 in renal fibrosis induced by unilateral ureter obstruction (UUO) or renal ischemia/reperfusion, which was accompanied by a significant decrease in mir-219a-5p expression. Functionally, overexpression of mir-219a-2 enhanced fibronectin induction during hypoxia or TGF-β1 treatment of cultured renal cells. In mice, inhibition of mir-219a-5p suppressed fibronectin accumulation in UUO kidneys. ALDH1L2 was identified to be the direct target gene of mir-219a-5p in renal fibrosis. Mir-219a-5p suppressed ALDH1L2 expression in cultured renal cells, while inhibition of mir-219a-5p prevented the decrease of ALDH1L2 in UUO kidneys. Knockdown of ALDH1L2 enhanced PAI-1 induction during TGF-β1 treatment of renal cells, which was associated with fibronectin expression. In conclusion, the hypermethylation of mir-219a-2 in response to fibrotic stress attenuates mir-219a-5p expression and induces the up-regulation of its target gene ALDH1L2, which may reduce fibronectin deposition by suppressing PAI-1.
Collapse
Affiliation(s)
- Xiao Xiao
- Zhongnan Hospital of Wuhan University
| | | | - Chunyuan Guo
- Shanghai Skin Disease Hospital, Tongji University School of Medicine
| | | | - Xiaoru Hu
- The Second Xiangya Hospital at Central South University
| | | | | | | | | |
Collapse
|
6
|
Hsueh YM, Chen WJ, Lee HL, Huang YL, Shiue HS, Hsu SL, Chen HH, Lin YC. Global DNA methylation and the association between metal exposure and chronic kidney disease. Front Public Health 2023; 11:1104692. [PMID: 37304094 PMCID: PMC10248129 DOI: 10.3389/fpubh.2023.1104692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 05/08/2023] [Indexed: 06/13/2023] Open
Abstract
Introduction Prior studies indicate that exposure to metals may alter DNA methylation. Evidence also shows that global DNA methylation is associated with chronic kidney disease (CKD). This study aimed to examine the association between CKD and 5-methyl-2-deoxycytidine (5mdC, %), a marker of global DNA methylation, and to evaluate the interaction between metal exposures and 5mdC (%) on CKD. We also explored the mediation effect of 5mdC (%) on the association between metal exposures and renal function (i.e., estimated glomerular filtration rate, eGFR). Methods A total of 218 CKD patients and 422 controls were recruited in this case-control study. 5mdC (%), concentrations of blood lead and cadmium, plasma selenium, and total urinary arsenic were measured. CKD cases were clinically defined among patients with eGFR <60 mL/min/1.73 m2 for at least 3 months and without hemodialysis. Odds ratio (OR) and 95% confidence interval (CI) were estimated by logistic regression models to examine the association between metal exposures, 5mdC (%), and CKD, adjusted for confounders. Multivariable linear regression models were used to examine associations between metal exposures, 5mdC (%), and eGFR. Results and Discussion CKD cases compared to controls had 6.06-fold (95% CI: 3.11-11.81) higher odds of having high blood cadmium and high 5mdC (%) levels. A positive interaction on an additive scale was identified between blood cadmium and 5mdC (%) on CKD. Cases compared to controls had 4.73-fold (95% CI: 2.65-8.45) higher odds of having low plasma selenium and high 5mdC (%) levels; and a significant multiplicative interaction between plasma selenium and 5mdC (%) on CKD was observed. In addition, we found that blood lead and cadmium concentrations were positively associated, while plasma selenium concentrations were inversely associated, with 5mdC (%). The associations of blood lead and plasma selenium with eGFR were partially mediated by 5mdC (%). Our results suggest that 5mdC (%) may interact with plasma selenium and blood cadmium to influence the risk of CKD. The 5mdC (%) also potentially mediates the associations between exposure to metals and renal function.
Collapse
Affiliation(s)
- Yu-Mei Hsueh
- Department of Family Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
- Department of Public Health, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Wei-Jen Chen
- Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, Houston, TX, United States
| | - Hui-Ling Lee
- Department of Chemistry, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Ya-Li Huang
- Department of Public Health, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Horng-Sheng Shiue
- Department of Chinese Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Sheng-Lun Hsu
- Department of Family Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Hsi-Hsien Chen
- Division of Nephrology, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Division of Nephrology, Department of Internal Medicine, Taipei Medical University Hospital, Taipei, Taiwan
| | - Ying-Chin Lin
- Department of Family Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
- Department of Family Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Department of Geriatric Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| |
Collapse
|
7
|
Coppola A, Lombari P, Mazzella E, Capolongo G, Simeoni M, Perna AF, Ingrosso D, Borriello M. Zebrafish as a Model of Cardiac Pathology and Toxicity: Spotlight on Uremic Toxins. Int J Mol Sci 2023; 24:ijms24065656. [PMID: 36982730 PMCID: PMC10052014 DOI: 10.3390/ijms24065656] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023] Open
Abstract
Chronic kidney disease (CKD) is an increasing health care problem. About 10% of the general population is affected by CKD, representing the sixth cause of death in the world. Cardiovascular events are the main mortality cause in CKD, with a cardiovascular risk 10 times higher in these patients than the rate observed in healthy subjects. The gradual decline of the kidney leads to the accumulation of uremic solutes with a negative effect on every organ, especially on the cardiovascular system. Mammalian models, sharing structural and functional similarities with humans, have been widely used to study cardiovascular disease mechanisms and test new therapies, but many of them are rather expensive and difficult to manipulate. Over the last few decades, zebrafish has become a powerful non-mammalian model to study alterations associated with human disease. The high conservation of gene function, low cost, small size, rapid growth, and easiness of genetic manipulation are just some of the features of this experimental model. More specifically, embryonic cardiac development and physiological responses to exposure to numerous toxin substances are similar to those observed in mammals, making zebrafish an ideal model to study cardiac development, toxicity, and cardiovascular disease.
Collapse
Affiliation(s)
- Annapaola Coppola
- Department of Advanced Medical and Surgical Sciences, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Patrizia Lombari
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Elvira Mazzella
- Department of Translational Medical Science, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Giovanna Capolongo
- Department of Translational Medical Science, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Mariadelina Simeoni
- Department of Translational Medical Science, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Alessandra F. Perna
- Department of Translational Medical Science, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Diego Ingrosso
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Margherita Borriello
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
- Correspondence:
| |
Collapse
|
8
|
Xie X, Li F, Xie L, Yu Y, Ou S, He R. Meta-analysis of cancer risk among end stage renal disease undergoing maintenance dialysis. Open Life Sci 2023; 18:20220553. [PMID: 36820211 PMCID: PMC9938539 DOI: 10.1515/biol-2022-0553] [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: 05/29/2022] [Revised: 11/15/2022] [Accepted: 11/30/2022] [Indexed: 02/19/2023] Open
Abstract
Currently, there is no consensus on whether maintenance dialysis increases cancer risk in patients with end-stage renal disease (ESRD). Therefore, this study was to systematically evaluate the risk of cancer among ESRD patients undergoing maintenance dialysis. Related studies on the impact of maintenance dialysis on cancer risk were retrieved from PubMed, Embase, Cochrane Library, and other databases from their respective inceptions to 19 February 2021. ESRD patients receiving maintenance dialysis were classified into cancer including non-melanoma skin cancer (NMSC) and cancer excluding NMSC. Standardized incidence ratio (SIR) with its 95% confidence interval (95% CI) was calculated to assess cancer risk. Fourteen studies were included in the meta-analysis. The risk of cancer in patients undergoing maintenance dialysis (with or without NMSC) was significantly higher than controls both in cancer including NMSC (SIR = 1.38, 95% CI: 1.27-1.49, P < 0.001) and cancer excluding NMSC (SIR = 1.34, 95% CI: 1.23-1.47, P < 0.001). Subgroup results identified the higher risk of cancer incidence in both men and women receiving maintenance dialysis. Meanwhile, elevated excess risks were observed among patients with younger age and shorter follow-up time (P < 0.001). Meanwhile, the combined SIR of bladder, cervix, colorectum, kidney, liver, thyroid, tongue, and other cancers were all increased (P < 0.05). ESRD patients undergoing dialysis has higher risk of cancer.
Collapse
Affiliation(s)
- Xin Xie
- Department of Nursing, The Affiliated Hospital of Southwest Medical University, Luzhou, China,Department of Nephrology, The Affiliated Hospital of Southwest Medical University, Luzhou, China,Sichuan Clinical Research Center for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Fang Li
- Department of Cardiology, People’s Hospital of Jianyang City, Jianyang, China
| | - Longsheng Xie
- Department of Nursing, The Affiliated Hospital of Southwest Medical University, Luzhou, China,Department of Nephrology, The Affiliated Hospital of Southwest Medical University, Luzhou, China,Sichuan Clinical Research Center for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Yanxia Yu
- Department of Nursing, The Affiliated Hospital of Southwest Medical University, Luzhou, China,Department of Nephrology, The Affiliated Hospital of Southwest Medical University, Luzhou, China,Sichuan Clinical Research Center for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Santao Ou
- Department of Nephrology, The Affiliated Hospital of Southwest Medical University, Luzhou, China,Sichuan Clinical Research Center for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Rongfang He
- Department of Nursing, The Affiliated Hospital of Southwest Medical University, Luzhou, China,Department of Psychiatry, The Affiliated Hospital of Southwest Medical University, No. 100 Taiping Street, Luzhou, Sichuan, 646000, China,Sichuan Clinical Research Center for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| |
Collapse
|
9
|
Smyth LJ, Dahlström EH, Syreeni A, Kerr K, Kilner J, Doyle R, Brennan E, Nair V, Fermin D, Nelson RG, Looker HC, Wooster C, Andrews D, Anderson K, McKay GJ, Cole JB, Salem RM, Conlon PJ, Kretzler M, Hirschhorn JN, Sadlier D, Godson C, Florez JC, Forsblom C, Maxwell AP, Groop PH, Sandholm N, McKnight AJ. Epigenome-wide meta-analysis identifies DNA methylation biomarkers associated with diabetic kidney disease. Nat Commun 2022; 13:7891. [PMID: 36550108 PMCID: PMC9780337 DOI: 10.1038/s41467-022-34963-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 11/14/2022] [Indexed: 12/24/2022] Open
Abstract
Type 1 diabetes affects over nine million individuals globally, with approximately 40% developing diabetic kidney disease. Emerging evidence suggests that epigenetic alterations, such as DNA methylation, are involved in diabetic kidney disease. Here we assess differences in blood-derived genome-wide DNA methylation associated with diabetic kidney disease in 1304 carefully characterised individuals with type 1 diabetes and known renal status from two cohorts in the United Kingdom-Republic of Ireland and Finland. In the meta-analysis, we identify 32 differentially methylated CpGs in diabetic kidney disease in type 1 diabetes, 18 of which are located within genes differentially expressed in kidneys or correlated with pathological traits in diabetic kidney disease. We show that methylation at 21 of the 32 CpGs predict the development of kidney failure, extending the knowledge and potentially identifying individuals at greater risk for diabetic kidney disease in type 1 diabetes.
Collapse
Affiliation(s)
- Laura J Smyth
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Emma H Dahlström
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Anna Syreeni
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Katie Kerr
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Jill Kilner
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Ross Doyle
- Diabetes Complications Research Centre, Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Eoin Brennan
- Diabetes Complications Research Centre, Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Viji Nair
- Department of Medicine-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI, 48109, USA
| | - Damian Fermin
- Department of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI, 48109, USA
| | - Robert G Nelson
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Helen C Looker
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Christopher Wooster
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Darrell Andrews
- Diabetes Complications Research Centre, Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Kerry Anderson
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Gareth J McKay
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Joanne B Cole
- Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Rany M Salem
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Peter J Conlon
- Department of Nephrology and Transplantation, Beaumont Hospital and Department of Medicine Royal College of Surgeons in Ireland, Dublin 9, Ireland
| | - Matthias Kretzler
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Joel N Hirschhorn
- Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics and Genetics, Harvard Medical School, Boston, MA, USA
| | | | - Catherine Godson
- Diabetes Complications Research Centre, Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Jose C Florez
- Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Carol Forsblom
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Alexander P Maxwell
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
- Regional Nephrology Unit, Belfast City Hospital, Belfast, Northern Ireland, UK
| | - Per-Henrik Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Niina Sandholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland.
| | - Amy Jayne McKnight
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK.
| |
Collapse
|
10
|
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.
Collapse
Affiliation(s)
| | | | | | | | - Amy Jayne McKnight
- Centre for Public Health, Queen’s University Belfast, Belfast, United Kingdom
| |
Collapse
|
11
|
Rysz J, Franczyk B, Rysz-Górzyńska M, Gluba-Brzózka A. Are Alterations in DNA Methylation Related to CKD Development? Int J Mol Sci 2022; 23:ijms23137108. [PMID: 35806113 PMCID: PMC9267048 DOI: 10.3390/ijms23137108] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/17/2022] [Accepted: 06/18/2022] [Indexed: 12/29/2022] Open
Abstract
The modifications in genomic DNA methylation are involved in the regulation of normal and pathological cellular processes. The epigenetic regulation stimulates biological plasticity as an adaptive response to variations in environmental factors. The role of epigenetic changes is vital for the development of some diseases, including atherogenesis, cancers, and chronic kidney disease (CKD). The results of studies presented in this review have suggested that altered DNA methylation can modulate the expression of pro-inflammatory and pro-fibrotic genes, as well those essential for kidney development and function, thus stimulating renal disease progression. Abnormally increased homocysteine, hypoxia, and inflammation have been suggested to alter epigenetic regulation of gene expression in CKD. Studies of renal samples have demonstrated the relationship between variations in DNA methylation and fibrosis and variations in estimated glomerular filtration rate (eGFR) in human CKD. The unravelling of the genetic–epigenetic profile would enhance our understanding of processes underlying the development of CKD. The understanding of multifaceted relationship between DNA methylation, genes expression, and disease development and progression could improve the ability to identify individuals at risk of CKD and enable the choice of appropriate disease management.
Collapse
Affiliation(s)
- Jacek Rysz
- Department of Nephrology, Hypertension and Family Medicine, Medical University of Lodz, 113 Żeromskego Street, 90-549 Lodz, Poland; (J.R.); (B.F.)
| | - Beata Franczyk
- Department of Nephrology, Hypertension and Family Medicine, Medical University of Lodz, 113 Żeromskego Street, 90-549 Lodz, Poland; (J.R.); (B.F.)
| | - Magdalena Rysz-Górzyńska
- Department of Otolaryngology, Laryngological Oncology, Audiology and Phoniatrics, Medical Univesity of Lodz, 113 Żeromskego Street, 90-549 Lodz, Poland;
| | - Anna Gluba-Brzózka
- Department of Nephrology, Hypertension and Family Medicine, Medical University of Lodz, 113 Żeromskego Street, 90-549 Lodz, Poland; (J.R.); (B.F.)
- Correspondence:
| |
Collapse
|
12
|
Ni L, Bai R, Zhou Q, Yuan C, Zhou LT, Wu X. The correlation between ferroptosis and m6A methylation in patients with acute kidney injury. Kidney Blood Press Res 2022; 47:523-533. [PMID: 35569444 DOI: 10.1159/000524900] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 04/23/2022] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE The present research analyzed the correlation between m6A methylation and ferroptosis associated genes (FAGs) in acute kidney injury (AKI) patients. METHODS Bioinformatics analysis of microarray profiles (GSE30718) were performed to select differential expression genes (DEGs). FAGs are derived from systematic analysis of the aberrances and functional implications. The m6A methylation related genes were derived from the molecular characterization and clinical significance of m6A modulators. The multi-gene correlation of ferroptosis and M6A methylation modification were displayed. Then, the CIBERSORT algorithm was used to analyse the proportions of 22 immune cells infiltration. RESULTS In total, 349 DEGs were extracted between the AKI and control samples, among which 172 genes were up-regulated and 177 were down-regulated. FAGs (SLC1A5, CARS, SAT1, ACSL4, NFE2L2, TFRC and MT1G) and m6A methylation related genes (YTHDF3, WTAP and IGF2BP3) were significantly increased in AKI patients (P< 0.05). FAGs (SAT1, ACSL4 and NFE2L2) was positively correlated with the expression level of m6A methylation genes (P< 0.05). NFE2L2 has high diagnostic value, and level of NFE2L2 was negatively correlated with the degree of follicular helper T (TFH) cells infiltration. CONCLUSION Our research could provide a new theoretical basis for the pathogenesis and immune mechanism of AKI.
Collapse
Affiliation(s)
- Lihua Ni
- Department of Nephrology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Rui Bai
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Qiuyuan Zhou
- Department of Nephrology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Pathology, The Central Hospital of Enshi Autonomous Prefecture, Enshi, China
| | - Cheng Yuan
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Le-Ting Zhou
- Department of Nephrology, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Xiaoyan Wu
- Department of Nephrology, Zhongnan Hospital of Wuhan University, Wuhan, China
| |
Collapse
|
13
|
Liu F, Chen J, Li Z, Meng X. Recent Advances in Epigenetics of Age-Related Kidney Diseases. Genes (Basel) 2022; 13:genes13050796. [PMID: 35627181 PMCID: PMC9142069 DOI: 10.3390/genes13050796] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 02/03/2023] Open
Abstract
Renal aging has attracted increasing attention in today’s aging society, as elderly people with advanced age are more susceptible to various kidney disorders such as acute kidney injury (AKI) and chronic kidney disease (CKD). There is no clear-cut universal mechanism for identifying age-related kidney diseases, and therefore, they pose a considerable medical and public health challenge. Epigenetics refers to the study of heritable modifications in the regulation of gene expression that do not require changes in the underlying genomic DNA sequence. A variety of epigenetic modifiers such as histone deacetylases (HDAC) inhibitors and DNA methyltransferase (DNMT) inhibitors have been proposed as potential biomarkers and therapeutic targets in numerous fields including cardiovascular diseases, immune system disease, nervous system diseases, and neoplasms. Accumulating evidence in recent years indicates that epigenetic modifications have been implicated in renal aging. However, no previous systematic review has been performed to systematically generalize the relationship between epigenetics and age-related kidney diseases. In this review, we aim to summarize the recent advances in epigenetic mechanisms of age-related kidney diseases as well as discuss the application of epigenetic modifiers as potential biomarkers and therapeutic targets in the field of age-related kidney diseases. In summary, the main types of epigenetic processes including DNA methylation, histone modifications, non-coding RNA (ncRNA) modulation have all been implicated in the progression of age-related kidney diseases, and therapeutic targeting of these processes will yield novel therapeutic strategies for the prevention and/or treatment of age-related kidney diseases.
Collapse
Affiliation(s)
- Feng Liu
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China;
| | - Jiefang Chen
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China;
| | - Zhenqiong Li
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China;
- Correspondence: (Z.L.); (X.M.)
| | - Xianfang Meng
- Department of Neurobiology, Institute of Brain Research, School of Basic Medical Sciences, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Correspondence: (Z.L.); (X.M.)
| |
Collapse
|
14
|
Xu H, Li S, Liu YS. Roles and Mechanisms of DNA Methylation in Vascular Aging and Related Diseases. Front Cell Dev Biol 2021; 9:699374. [PMID: 34262910 PMCID: PMC8273304 DOI: 10.3389/fcell.2021.699374] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/07/2021] [Indexed: 12/20/2022] Open
Abstract
Vascular aging is a pivotal risk factor promoting vascular dysfunction, the development and progression of vascular aging-related diseases. The structure and function of endothelial cells (ECs), vascular smooth muscle cells (VSMCs), fibroblasts, and macrophages are disrupted during the aging process, causing vascular cell senescence as well as vascular dysfunction. DNA methylation, an epigenetic mechanism, involves the alteration of gene transcription without changing the DNA sequence. It is a dynamically reversible process modulated by methyltransferases and demethyltransferases. Emerging evidence reveals that DNA methylation is implicated in the vascular aging process and plays a central role in regulating vascular aging-related diseases. In this review, we seek to clarify the mechanisms of DNA methylation in modulating ECs, VSMCs, fibroblasts, and macrophages functions and primarily focus on the connection between DNA methylation and vascular aging-related diseases. Therefore, we represent many vascular aging-related genes which are modulated by DNA methylation. Besides, we concentrate on the potential clinical application of DNA methylation to serve as a reliable diagnostic tool and DNA methylation-based therapeutic drugs for vascular aging-related diseases.
Collapse
Affiliation(s)
- Hui Xu
- Department of Geriatrics, The Second Xiangya Hospital, Central South University, Changsha, China.,Institute of Aging and Age-Related Disease Research, Central South University, Changsha, China
| | - Shuang Li
- Department of Geriatrics, The Second Xiangya Hospital, Central South University, Changsha, China.,Institute of Aging and Age-Related Disease Research, Central South University, Changsha, China
| | - You-Shuo Liu
- Department of Geriatrics, The Second Xiangya Hospital, Central South University, Changsha, China.,Institute of Aging and Age-Related Disease Research, Central South University, Changsha, China
| |
Collapse
|