Dataset Information

Mendelian Randomization Identifies CpG Methylation Sites With Mediation Effects for Genetic Influences on BMD in Peripheral Blood Monocytes.

ABSTRACT: Osteoporosis is mainly characterized by low bone mineral density (BMD) and is an increasingly serious public health concern. DNA methylation is a major epigenetic mechanism that may contribute to the variation in BMD and may mediate the effects of genetic and environmental factors of osteoporosis. In this study, we performed an epigenome-wide DNA methylation analysis in peripheral blood monocytes of 118 Caucasian women with extreme BMD values. Further, we developed and implemented a novel analytical framework that integrates Mendelian randomization with genetic fine mapping and colocalization to evaluate the causal relationships between DNA methylation and BMD phenotype. We identified 2,188 differentially methylated CpGs (DMCs) between the low and high BMD groups and distinguished 30 DMCs that may mediate the genetic effects on BMD. The causal relationship was further confirmed by eliminating the possibility of horizontal pleiotropy, linkage effect and reverse causality. The fine-mapping analysis determined 25 causal variants that are most likely to affect the methylation levels at these mediator DMCs. The majority of the causal methylation quantitative loci and DMCs reside within cell type-specific histone mark peaks, enhancers, promoters, promoter flanking regions and CTCF binding sites, supporting the regulatory potentials of these loci. The established causal pathways from genetic variant to BMD phenotype mediated by DNA methylation provide a gene list to aid in designing future functional studies and lead to a better understanding of the genetic and epigenetic mechanisms underlying the variation of BMD.

SUBMITTER: Yu F

PROVIDER: S-EPMC7059767 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Mendelian Randomization Identifies CpG Methylation Sites With Mediation Effects for Genetic Influences on BMD in Peripheral Blood Monocytes.

Yu Fangtang F Qiu Chuan C Xu Chao C Tian Qing Q Zhao Lan-Juan LJ Wu Li L Deng Hong-Wen HW Shen Hui H

Frontiers in genetics 20200228

Osteoporosis is mainly characterized by low bone mineral density (BMD) and is an increasingly serious public health concern. DNA methylation is a major epigenetic mechanism that may contribute to the variation in BMD and may mediate the effects of genetic and environmental factors of osteoporosis. In this study, we performed an epigenome-wide DNA methylation analysis in peripheral blood monocytes of 118 Caucasian women with extreme BMD values. Further, we developed and implemented a novel analyt ...[more]

PMID: 32180791

Similar Datasets

Project description:Background and objectivesFatigue has been associated with adverse effects on recovery from ischemic stroke based on previous observational research. The purpose of our study was to explore the potential causal association of fatigue with poor functional outcome after ischemic stroke by employing Mendelian randomization (MR).MethodsA set of instrumental variables, comprising 36 single-nucleotide polymorphisms (SNPs) that are only related to fatigue, were derived from a genome-wide association study (GWAS) that included 449,019 general individuals. The functional outcomes after ischemic stroke were derived from a GWAS (Genetics of Ischemic Stroke Functional Outcome Network) involving 6,021 survivors. Two-sample MR methods were used to assess the causal effect, including inverse variance weighted, MR-Egger, weighted median, simple mode, and weighted mode. In bidirectional MR analysis, the reverse causal association was analyzed using the Wald ratio method. The mediation effects of lipid metabolites were analyzed using two-step MR analysis.ResultsGenetic liability to fatigue was causally associated with the poor functional outcome (modified Rankin Scale ≥3 at 3 months) after ischemic stroke (OR = 4.20, 95%CI [1.11-15.99], p < 0.05). However, genetic predicted poor functional outcome after ischemic stroke was not associated with fatigue (OR = 1.00, 95%CI [0.99-1.02], p > 0.05). The results of the two-step MR showed that cholesteryl esters to total lipids ratio in large very low-density lipoprotein (VLDL) (ME = -0.13, p < 0.05); concentration of very large VLDL particles (ME = -0.13, p < 0.05); free cholesterol in large VLDL (ME = -0.13, p < 0.05); free cholesterol to total lipids ratio in very large VLDL (ME = -0.22, p < 0.05); phospholipids in large VLDL (ME = -0.15, p < 0.05); phospholipids in very large VLDL (ME = -0.13, p < 0.05); phospholipids to total lipids ratio in large high-density lipoprotein (HDL) (ME = -0.17, p < 0.05); total lipids in very large VLDL (ME = -0.14, p < 0.05); triglycerides in small VLDL (ME = -0.11, p < 0.05); and triglycerides to total lipids ratio in large HDL (ME = -0.10, p < 0.05) assumed a pivotal role in mediating the association between fatigue and poor functional outcome after ischemic stroke.ConclusionOur study provides evidence supporting the causal association between fatigue and the poor functional outcome after ischemic stroke, which emphasizes the importance of implementing interventions aimed at addressing fatigue. This could offer a therapeutic target to improve recovery after ischemic stroke and warrant exploration in a clinical context. One potential mechanism by which fatigue affects functional outcomes after ischemic stroke is through the action of lipid metabolites.

Dataset Information

Mendelian Randomization Identifies CpG Methylation Sites With Mediation Effects for Genetic Influences on BMD in Peripheral Blood Monocytes.

Publications

Mendelian Randomization Identifies CpG Methylation Sites With Mediation Effects for Genetic Influences on BMD in Peripheral Blood Monocytes.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets