1
|
Qiu C, Hanson RL, Fufaa G, Kobes S, Gluck C, Huang J, Chen Y, Raj D, Nelson RG, Knowler WC, Susztak K. Cytosine methylation predicts renal function decline in American Indians. Kidney Int 2018; 93:1417-1431. [PMID: 29709239 PMCID: PMC5973533 DOI: 10.1016/j.kint.2018.01.036] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 01/07/2018] [Accepted: 01/25/2018] [Indexed: 12/18/2022]
Abstract
Diabetic nephropathy accounts for most of the excess mortality in individuals with diabetes, but the molecular mechanisms by which nephropathy develops are largely unknown. Here we tested cytosine methylation levels at 397,063 genomic CpG sites for association with decline in the estimated glomerular filtration rate (eGFR) over a six year period in 181 diabetic Pima Indians. Methylation levels at 77 sites showed significant association with eGFR decline after correction for multiple comparisons. A model including methylation level at two probes (cg25799291 and cg22253401) improved prediction of eGFR decline in addition to baseline eGFR and the albumin to creatinine ratio with the percent of variance explained significantly improving from 23.1% to 42.2%. Cg22253401 was also significantly associated with eGFR decline in a case-control study derived from the Chronic Renal Insufficiency Cohort. Probes at which methylation significantly associated with eGFR decline were localized to gene regulatory regions and enriched for genes with metabolic functions and apoptosis. Three of the 77 probes that were associated with eGFR decline in blood samples showed directionally consistent and significant association with fibrosis in microdissected human kidney tissue, after correction for multiple comparisons. Thus, cytosine methylation levels may provide biomarkers of disease progression in diabetic nephropathy and epigenetic variations contribute to the development of diabetic kidney disease.
Collapse
MESH Headings
- Adult
- Aged
- Albuminuria/ethnology
- Albuminuria/genetics
- Albuminuria/physiopathology
- Apoptosis/genetics
- Case-Control Studies
- Cell Cycle/genetics
- CpG Islands
- Cytosine
- DNA Methylation
- Diabetic Nephropathies/diagnosis
- Diabetic Nephropathies/ethnology
- Diabetic Nephropathies/genetics
- Diabetic Nephropathies/physiopathology
- Disease Progression
- Energy Metabolism/genetics
- Epigenesis, Genetic
- Female
- Fibrosis
- Genetic Predisposition to Disease
- Glomerular Filtration Rate/genetics
- Humans
- Indians, North American/genetics
- Kidney/pathology
- Kidney/physiopathology
- Kidney Failure, Chronic/diagnosis
- Kidney Failure, Chronic/ethnology
- Kidney Failure, Chronic/genetics
- Kidney Failure, Chronic/physiopathology
- Male
- Middle Aged
- Phenotype
- Prognosis
- Renal Insufficiency, Chronic/diagnosis
- Renal Insufficiency, Chronic/ethnology
- Renal Insufficiency, Chronic/genetics
- Renal Insufficiency, Chronic/physiopathology
- Risk Factors
Collapse
Affiliation(s)
- Chengxiang Qiu
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Robert L Hanson
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, Arizona, USA.
| | - Gudeta Fufaa
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, Arizona, USA
| | - Sayuko Kobes
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, Arizona, USA
| | - Caroline Gluck
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Jing Huang
- Department of Biostatistics, Epidemiology and Informatics, Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Yong Chen
- Department of Biostatistics, Epidemiology and Informatics, Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Dominic Raj
- Division of Renal Diseases and Hypertension, The George Washington School of Medicine, Washington, DC, USA
| | - Robert G Nelson
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, Arizona, USA
| | - William C Knowler
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, Arizona, USA
| | - Katalin Susztak
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| |
Collapse
|
2
|
Abstract
PURPOSE OF REVIEW It is becoming increasingly evident that epigenetic mechanisms, particularly DNA methylation, play a role in the regulation of blood lipid levels and lipid metabolism-linked phenotypes and diseases. RECENT FINDINGS Recent genome-wide methylation and candidate gene studies of blood lipids have highlighted several robustly replicated methylation markers across different ethnicities. Furthermore, many of these lipid-related CpG sites associated with blood lipids are also linked to lipid-related phenotypes and diseases. Integrating epigenome-wide association studies (EWAS) data with other layers of molecular data such as genetics or the transcriptome, accompanied by relevant statistical methods (e.g. Mendelian randomization), provides evidence for causal relationships. Recent data suggest that epigenetic changes can be consequences rather than causes of dyslipidemia. There is sparse information on many lipid classes and disorders of lipid metabolism, and also on the interplay of DNA methylation with other epigenetic layers such as histone modifications and regulatory RNAs. SUMMARY The current review provides a literature overview of epigenetic modifications in lipid metabolism and other lipid-related phenotypes and diseases focusing on EWAS of DNA methylation from January 2016 to September 2017. Recent studies strongly support the importance of epigenetic modifications, such as DNA methylation, in lipid metabolism and related diseases for relevant biological insights, reliable biomarkers, and even future therapeutics.
Collapse
Affiliation(s)
- Kirstin Mittelstraß
- Research Unit of Molecular Epidemiology
- Institute of Epidemiology, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology
- Institute of Epidemiology, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
| |
Collapse
|
3
|
Zhang S, Shen L, Xia Y, Yang Q, Li X, Tang G, Jiang Y, Wang J, Li M, Zhu L. DNA methylation landscape of fat deposits and fatty acid composition in obese and lean pigs. Sci Rep 2016; 6:35063. [PMID: 27721392 PMCID: PMC5056348 DOI: 10.1038/srep35063] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 09/23/2016] [Indexed: 01/19/2023] Open
Abstract
Obese and lean type pig breeds exhibit differences in their fat deposits and fatty acid composition. Here, we compared the effect of genome-wide DNA methylation on fatty acid metabolism between Landrace pigs (LP, leaner) and Rongchang pigs (RP, fatty). We found that LP backfat (LBF) had a higher polyunsaturated fatty acid content but a lower adipocyte volume than RP backfat (RBF). LBF exhibited higher global DNA methylation levels at the genome level than RBF. A total of 483 differentially methylated regions (DMRs) were located in promoter regions, mainly affecting olfactory and sensory activity and lipid metabolism. In LBF, the promoters of genes related to ATPase activity had significantly stronger methylation. This fact may suggest lower energy metabolism levels, which may result in less efficient lipid synthesis in LBF. Furthermore, we identified a DMR in the miR-4335 and miR-378 promoters and validated their methylation status by bisulfite sequencing PCR. The hypermethylation of the promoters of miR-4335 and miR-378 in LBF and the resulting silencing of the target genes may result in LBF's low content in saturated fatty acids and fat deposition capacity. This study provides a solid basis for exploring the epigenetic mechanisms affecting fat deposition and fatty acid composition.
Collapse
Affiliation(s)
- Shunhua Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Linyuan Shen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | | | - Qiong Yang
- Department of Animal Husbandry and Veterinary Medicine, Chengdu Agricultural College, Chengdu, Sichuan, China
| | - Xuewei Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Guoqing Tang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yanzhi Jiang
- Department of Biology, College of Life and Science, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jinyong Wang
- Chongqing Academy of Animal Science, Rongchang, Chongqing, China
| | - Mingzhou Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Li Zhu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| |
Collapse
|