Abstract P098: An Epigenome-wide Study of Obesity in African American Youth and Young Adults: Novel Findings, Replication in Neutrophils and Relationship With Gene Expression

Background: Several large-scale epigenome wide association studies on obesity-related DNA methylation changes have been published and in total identified 46 CpG sites. These studies were conducted in middle-aged and older adults of Caucasians and African Americans (AAs) using leukocytes. To what extend these signals are independent of cell compositions as well as to what extend they may influence gene expression have not been systematically investigated. Furthermore, the high prevalence of obesity comorbidities in middle-aged or older population may hide or bias obesity itself related DNA methylation changes. Methods: In this study of healthy AA youth and young adults, genome wide DNA methylation data from leukocytes were obtained from three independent studies: EpiGO study (96 obese cases vs. 92 lean controls, aged 14-21, 50% females, test of interest is obesity status), LACHY study (284 participants from general population, aged 14-18, 50% females, test of interest is BMI), and Georgia Stress and Heart study (298 participants from general population, aged 18-38, 52% females, test of interest is BMI) using the Infinium HumanMethylation450 BeadChip. Genome wide DNA methylation data from purified neutrophils as well as genome wide gene expression data from leukocytes using Illumina HT12 V4 array were also obtained for the EpiGO samples. Results: The meta-analysis on the 3 cohorts identified 76 obesity related CpG sites in leukocytes with p<1х10 -7 . Out of the 46 previously identified CpG sites, 36 can be replicated in this AA youth and young adult sample with same direction and p<0.05. Out of the 107 CpG sites including the 36 replicated ones and the 71 newly identified ones, 71 CpG sites (66%) had their relationship with obesity replicated in purified neutrophils (p<0.05). The analysis on the cis regulation of the 107 CpG sites on gene expression showed that 59 CpG sites had at least one gene within 250kb having expression difference between obese cases and lean controls. Furthermore, out of the 59 CpG sites, 6 showed significantly negative correlations and 1 showed significantly positive correlation with the differentially expressed genes. These CpG sites located in SOCS3, CISH, ABCG1, PIM3 and PTGDS genes. Conclusion: In this study of AA youth and young adults, we identified novel CpG sites associated with obesity and replicated majority of the CpG sites previously identified in middle-aged and older adults. For the first time, we showed that majority of the obesity related CpG sites identified from leukocytes are not driven by cell compositions and provided the direct link between DNA methylation-gene expression-obesity status for 7 CpG sites in 5 genes.

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Abstract MP55: DNA Methylation Mediates The Effects Of Obesity On Insulin Resistance In African American Youth And Young Adults

Circulation ◽

10.1161/circ.129.suppl_1.mp55 ◽

2014 ◽

Vol 129 (suppl_1) ◽

Author(s):

Xiaojing Xu ◽

Shaoyong Su ◽

Vernon Barnes ◽

Harold Snieder ◽

Xiaoling Wang

Keyword(s):

Insulin Resistance ◽

Dna Methylation ◽

Young Adults ◽

African American ◽

African American Youth ◽

Fasting Insulin ◽

Cpg Sites ◽

Cpg Site ◽

Genome Wide ◽

Youth And Young Adults

Obesity and its related cardiovascular disease and type 2 diabetes have imposed huge burdens on public health worldwide. Insulin resistance is considered one of the key players in the development of obesity related comorbidities. However, the underlying mechanisms are still largely unknown. In this study, we aim to examine whether and to what extent peripheral blood DNA methylation can mediate obesity’s effect on insulin resistance using a genome-wide approach. Illumina 450k data were obtained for 456 black youth and young adults (226 obese cases vs. 230 lean controls) aged 14-34 years with fasting insulin levels available for 293 subjects and genome-wide gene expression data available for 92 subjects. As shown in figure 1, obesity and fasting insulin associated differentially methylated CpG sites were identified separately. Among the overlap of these 2 lists (n=69), 32 CpG sites mapping to 28 genes significantly mediated obesity’s effect on fasting insulin. Principal component analysis found that, in total, these 32 methylation sites explained up to 17.3% of the effect of obesity on insulin. Among these mediators, the top CpG site is located in the promoter region of the LIPA (lipase A) gene, and this single CpG site explained 8.4% of the effect of obesity on insulin. Consistent with the higher methylation levels observed in the obese group, LIPA expression was decreased in the obese group (p=0.038). A significant negative partial correlation was also found between LIPA methylation levels and its expression levels (p=0.01, r=-0.26). Genetic variants in LIPA have been suggested to contribute to the interindividual variability in metabolic traits observed among obese individuals. In summary, we observed that peripheral blood DNA methylation mediates obesity’s effect on insulin resistance in African American youth and young adults, explaining up to 17% of the effect.

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Age-related differences in monocyte DNA methylation and immune function in healthy Kenyan adults and children

Immunity & Ageing ◽

10.1186/s12979-021-00223-2 ◽

2021 ◽

Vol 18 (1) ◽

Author(s):

Katherine R. Dobbs ◽

Paula Embury ◽

Emmily Koech ◽

Sidney Ogolla ◽

Stephen Munga ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Young Adults ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Innate Immune ◽

Inflammatory Gene Expression ◽

Cpg Sites ◽

Age Related ◽

Adults And Children

Abstract Background Age-related changes in adaptive and innate immune cells have been associated with a decline in effective immunity and chronic, low-grade inflammation. Epigenetic, transcriptional, and functional changes in monocytes occur with aging, though most studies to date have focused on differences between young adults and the elderly in populations with European ancestry; few data exist regarding changes that occur in circulating monocytes during the first few decades of life or in African populations. We analyzed DNA methylation profiles, cytokine production, and inflammatory gene expression profiles in monocytes from young adults and children from western Kenya. Results We identified several hypo- and hyper-methylated CpG sites in monocytes from Kenyan young adults vs. children that replicated findings in the current literature of differential DNA methylation in monocytes from elderly persons vs. young adults across diverse populations. Differentially methylated CpG sites were also noted in gene regions important to inflammation and innate immune responses. Monocytes from Kenyan young adults vs. children displayed increased production of IL-8, IL-10, and IL-12p70 in response to TLR4 and TLR2/1 stimulation as well as distinct inflammatory gene expression profiles. Conclusions These findings complement previous reports of age-related methylation changes in isolated monocytes and provide novel insights into the role of age-associated changes in innate immune functions.

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Changes in DNA Methylation and Gene Expression of Insulin and Obesity-Related Gene PIK3R1 after Roux-en-Y Gastric Bypass

International Journal of Molecular Sciences ◽

10.3390/ijms21124476 ◽

2020 ◽

Vol 21 (12) ◽

pp. 4476

Author(s):

Marcela A S Pinhel ◽

Natália Y Noronha ◽

Carolina F Nicoletti ◽

Vanessa AB Pereira ◽

Bruno AP de Oliveira ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Weight Loss ◽

Gastric Bypass ◽

Related Gene ◽

Cpg Sites ◽

Genome Wide ◽

Genetically Determined ◽

Methylation Patterns ◽

Weight Loss Interventions

Weight regulation and the magnitude of weight loss after a Roux-en-Y gastric bypass (RYGB) can be genetically determined. DNA methylation patterns and the expression of some genes can be altered after weight loss interventions, including RYGB. The present study aimed to evaluate how the gene expression and DNA methylation of PIK3R1, an obesity and insulin-related gene, change after RYGB. Blood samples were obtained from 13 women (35.9 ± 9.2 years) with severe obesity before and six months after surgical procedure. Whole blood transcriptome and epigenomic patterns were assessed by microarray-based, genome-wide technologies. A total of 1966 differentially expressed genes were identified in the pre- and postoperative periods of RYGB. From these, we observed that genes involved in obesity and insulin pathways were upregulated after surgery. Then, the PIK3R1 gene was selected for further RT-qPCR analysis and cytosine-guanine nucleotide (CpG) sites methylation evaluation. We observed that the PI3KR1 gene was upregulated, and six DNA methylation CpG sites were differently methylated after bariatric surgery. In conclusion, we found that RYGB upregulates genes involved in obesity and insulin pathways.

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Testing cell-type-specific mediation effects in genome-wide epigenetic studies

Briefings in Bioinformatics ◽

10.1093/bib/bbaa131 ◽

2020 ◽

Cited By ~ 1

Author(s):

Xiangyu Luo ◽

Joel Schwartz ◽

Andrea Baccarelli ◽

Zhonghua Liu

Keyword(s):

Dna Methylation ◽

Mediation Analysis ◽

Methylation Data ◽

Cell Type ◽

Multiple Testing Procedure ◽

Mediation Effects ◽

Cpg Sites ◽

Genome Wide ◽

A Cell ◽

Cell Type Specific

Abstract Epigenome-wide mediation analysis aims to identify DNA methylation CpG sites that mediate the causal effects of genetic/environmental exposures on health outcomes. However, DNA methylations in the peripheral blood tissues are usually measured at the bulk level based on a heterogeneous population of white blood cells. Using the bulk level DNA methylation data in mediation analysis might cause confounding bias and reduce study power. Therefore, it is crucial to get fine-grained results by detecting mediation CpG sites in a cell-type-specific way. However, there is a lack of methods and software to achieve this goal. We propose a novel method (Mediation In a Cell-type-Specific fashion, MICS) to identify cell-type-specific mediation effects in genome-wide epigenetic studies using only the bulk-level DNA methylation data. MICS follows the standard mediation analysis paradigm and consists of three key steps. In step1, we assess the exposure-mediator association for each cell type; in step 2, we assess the mediator-outcome association for each cell type; in step 3, we combine the cell-type-specific exposure-mediator and mediator-outcome associations using a multiple testing procedure named MultiMed [Sampson JN, Boca SM, Moore SC, et al. FWER and FDR control when testing multiple mediators. Bioinformatics 2018;34:2418–24] to identify significant CpGs with cell-type-specific mediation effects. We conduct simulation studies to demonstrate that our method has correct FDR control. We also apply the MICS procedure to the Normative Aging Study and identify nine DNA methylation CpG sites in the lymphocytes that might mediate the effect of cigarette smoking on the lung function.

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The Expression Level of mRNA, Protein, and DNA Methylation Status of FOSL2 of Uyghur in XinJiang in Type 2 Diabetes

Journal of Diabetes Research ◽

10.1155/2016/5957404 ◽

2016 ◽

Vol 2016 ◽

pp. 1-7 ◽

Cited By ~ 2

Author(s):

Jun Li ◽

Siyuan Li ◽

Ying Hu ◽

Guolei Cao ◽

Siyao Wang ◽

...

Keyword(s):

Gene Expression ◽

Type 2 Diabetes ◽

Dna Methylation ◽

Methylation Status ◽

Methylation Data ◽

Biochemical Indicators ◽

Expression Levels ◽

Protein Levels ◽

Cpg Sites

Objective. We investigated the expression levels of both FOSL2 mRNA and protein as well as evaluating DNA methylation in the blood of type 2 diabetes mellitus (T2DM) Uyghur patients from Xinjiang. This study also evaluated whether FOSL2 gene expression had demonstrated any associations with clinical and biochemical indicators of T2DM. Methods. One hundred Uyghur subjects where divided into two groups, T2DM and nonimpaired glucose tolerance (NGT) groups. DNA methylation of FOSL2 was also analyzed by MassARRAY Spectrometry and methylation data of individual units were generated by the EpiTyper v1.0.5 software. The expression levels of FOS-like antigen 2 (FOSL2) and the protein expression levels were analyzed. Results. Significant differences were observed in mRNA and protein levels when compared with the NGT group, while methylation rates of eight CpG units within the FOSL2 gene were higher in the T2DM group. Methylation of CpG sites was found to inversely correlate with expression of other markers. Conclusions. Results show that a correlation between mRNA, protein, and DNA methylation of FOSL2 gene exists among T2DM patients from Uyghur. FOSL2 protein and mRNA were downregulated and the DNA became hypermethylated, all of which may be involved in T2DM pathogenesis in this population.

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Genome-Wide DNA Methylation Analysis Shows Enrichment of Differential Methylation in “Open Seas” and Enhancers and Reveals Hypomethylation in DNMT3A Mutated Cytogenetically Normal AML (CN-AML)

Blood ◽

10.1182/blood.v120.21.653.653 ◽

2012 ◽

Vol 120 (21) ◽

pp. 653-653 ◽

Cited By ~ 2

Author(s):

Ying Qu ◽

Andreas Lennartsson ◽

Verena I. Gaidzik ◽

Stefan Deneberg ◽

Sofia Bengtzén ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Cpg Island ◽

Cpg Islands ◽

Differential Methylation ◽

Methylation Analysis ◽

Cpg Sites ◽

Genome Wide ◽

Genomic Regions ◽

Methylation Patterns

Abstract Abstract 653 DNA methylation is involved in multiple biologic processes including normal cell differentiation and tumorigenesis. In AML, methylation patterns have been shown to differ significantly from normal hematopoietic cells. Most studies of DNA methylation in AML have previously focused on CpG islands within the promoter of genes, representing only a very small proportion of the DNA methylome. In this study, we performed genome-wide methylation analysis of 62 AML patients with CN-AML and CD34 positive cells from healthy controls by Illumina HumanMethylation450K Array covering 450.000 CpG sites in CpG islands as well as genomic regions far from CpG islands. Differentially methylated CpG sites (DMS) between CN-AML and normal hematopoietic cells were calculated and the most significant enrichment of DMS was found in regions more than 4kb from CpG Islands, in the so called open sea where hypomethylation was the dominant form of aberrant methylation. In contrast, CpG islands were not enriched for DMS and DMS in CpG islands were dominated by hypermethylation. DMS successively further away from CpG islands in CpG island shores (up to 2kb from CpG Island) and shelves (from 2kb to 4kb from Island) showed increasing degree of hypomethylation in AML cells. Among regions defined by their relation to gene structures, CpG dinucleotide located in theoretic enhancers were found to be the most enriched for DMS (Chi χ2<0.0001) with the majority of DMS showing decreased methylation compared to CD34 normal controls. To address the relation to gene expression, GEP (gene expression profiling) by microarray was carried out on 32 of the CN-AML patients. Totally, 339723 CpG sites covering 18879 genes were addressed on both platforms. CpG methylation in CpG islands showed the most pronounced anti-correlation (spearman ρ =-0.4145) with gene expression level, followed by CpG island shores (mean spearman rho for both sides' shore ρ=-0.2350). As transcription factors (TFs) have shown to be crucial for AML development, we especially studied differential methylation of an unbiased selection of 1638 TFs. The most enriched differential methylation between CN-AML and normal CD34 positive cells were found in TFs known to be involved in hematopoiesis and with Wilms tumor protein-1 (WT1), activator protein 1 (AP-1) and runt-related transcription factor 1 (RUNX1) being the most differentially methylated TFs. The differential methylation in WT 1 and RUNX1 was located in intragenic regions which were confirmed by pyro-sequencing. AML cases were characterized with respect to mutations in FLT3, NPM1, IDH1, IDH2 and DNMT3A. Correlation analysis between genome wide methylation patterns and mutational status showed statistically significant hypomethylation of CpG Island (p<0.0001) and to a lesser extent CpG island shores (p<0.001) and the presence of DNMT3A mutations. This links DNMT3A mutations for the first time to a hypomethylated phenotype. Further analyses correlating methylation patterns to other clinical data such as clinical outcome are ongoing. In conclusion, our study revealed that non-CpG island regions and in particular enhancers are the most aberrantly methylated genomic regions in AML and that WT 1 and RUNX1 are the most differentially methylated TFs. Furthermore, our data suggests a hypomethylated phenotype in DNMT3A mutated AML. Disclosures: No relevant conflicts of interest to declare.

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Age-related Differences in Monocyte DNA Methylation and Immune Function in Healthy Kenyan Adults and Children

10.21203/rs.3.rs-80601/v1 ◽

2020 ◽

Author(s):

Katherine Rose Dobbs ◽

Paula Embury ◽

Emmily Koech ◽

Sidney Ogolla ◽

Stephen Munga ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Young Adults ◽

Innate Immune ◽

European Ancestry ◽

Inflammatory Gene Expression ◽

Inflammatory Gene ◽

Cpg Sites ◽

Age Related ◽

Adults And Children

Abstract Background: Age-related changes in adaptive and innate immune cells have been associated with a decline in effective immunity and chronic, low-grade inflammation. Epigenetic, transcriptional, and functional changes in monocytes occur with aging, though most studies to date have focused on differences between young adults and the elderly in populations with European ancestry; few data exist regarding changes that occur in circulating monocytes during the first few decades of life or in African populations. We analyzed DNA methylation profiles, cytokine production, and inflammatory gene expression profi 24 les in monocytes from young adults and children from western Kenya.Results: We identified several hypo- and hyper-methylated CpG sites in monocytes from Kenyan young adults vs. children that replicated findings in the current literature of differential DNA methylation in monocytes from elderly persons vs. young adults across diverse populations. Differentially methylated CpG sites were also noted in gene regions important to inflammation and innate immune responses. Monocytes from Kenyan young adults vs. children displayed increased production of IL-8, IL-10, and IL-12p70 in response to TLR4 and TLR2/1 stimulation as well as distinct inflammatory gene expression profiles.Conclusions: These findings complement previous reports of age-related methylation changes in isolated monocytes and provide novel insights into the role of age-associated changes in innate immune functions.

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Genome-wide DNA methylation analysis of pulmonary function in middle and old-aged Chinese monozygotic twins

Respiratory Research ◽

10.1186/s12931-021-01896-5 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Tong Wang ◽

Weijing Wang ◽

Weilong Li ◽

Haiping Duan ◽

Chunsheng Xu ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Pulmonary Function ◽

Monozygotic Twins ◽

Linear Mixed Effect Model ◽

Sequencing Analysis ◽

Mixed Effect ◽

Cpg Sites ◽

Genome Wide ◽

Genomic Regions

Abstract Background Previous studies have determined the epigenetic association between DNA methylation and pulmonary function among various ethnics, whereas this association is largely unknown in Chinese adults. Thus, we aimed to explore epigenetic relationships between genome-wide DNA methylation levels and pulmonary function among middle-aged Chinese monozygotic twins. Methods The monozygotic twin sample was drawn from the Qingdao Twin Registry. Pulmonary function was measured by three parameters including forced expiratory volume the first second (FEV1), forced vital capacity (FVC), and FEV1/FVC ratio. Linear mixed effect model was used to regress the methylation level of CpG sites on pulmonary function. After that, we applied Genomic Regions Enrichment of Annotations Tool (GREAT) to predict the genomic regions enrichment, and used comb-p python library to detect differentially methylated regions (DMRs). Gene expression analysis was conducted to validate the results of differentially methylated analyses. Results We identified 112 CpG sites with the level of P < 1 × 10–4 which were annotated to 40 genes. We identified 12 common enriched pathways of three pulmonary function parameters. We detected 39 DMRs located at 23 genes, of which PRDM1 was related to decreased pulmonary function, and MPL, LTB4R2, and EPHB3 were related to increased pulmonary function. The gene expression analyses validated DIP2C, ASB2, SLC6A5, and GAS6 related to decreased pulmonary function. Conclusion Our DNA methylation sequencing analysis on identical twins provides new references for the epigenetic regulation on pulmonary function. Several CpG sites, genes, biological pathways and DMRs are considered as possible crucial to pulmonary function.

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Identification, Heritability, and Relation With Gene Expression of Novel DNA Methylation Loci for Blood Pressure

Hypertension ◽

10.1161/hypertensionaha.120.14973 ◽

2020 ◽

Vol 76 (1) ◽

pp. 195-205 ◽

Cited By ~ 1

Author(s):

Yisong Huang ◽

Miina Ollikainen ◽

Maheswary Muniandy ◽

Tao Zhang ◽

Jenny van Dongen ◽

...

Keyword(s):

Gene Expression ◽

Blood Pressure ◽

Dna Methylation ◽

Association Study ◽

Meta Analysis ◽

African Ancestry ◽

Cpg Sites ◽

Genome Wide ◽

Novel Association ◽

Peripheral Leukocytes

We conducted an epigenome-wide association study meta-analysis on blood pressure (BP) in 4820 individuals of European and African ancestry aged 14 to 69. Genome-wide DNA methylation data from peripheral leukocytes were obtained using the Infinium Human Methylation 450k BeadChip. The epigenome-wide association study meta-analysis identified 39 BP-related CpG sites with P <1×10 −5 . In silico replication in the CHARGE consortium of 17 010 individuals validated 16 of these CpG sites. Out of the 16 CpG sites, 13 showed novel association with BP. Conversely, out of the 126 CpG sites identified as being associated ( P <1×10 −7 ) with BP in the CHARGE consortium, 21 were replicated in the current study. Methylation levels of all the 34 CpG sites that were cross-validated by the current study and the CHARGE consortium were heritable and 6 showed association with gene expression. Furthermore, 9 CpG sites also showed association with BP with P <0.05 and consistent direction of the effect in the meta-analysis of the Finnish Twin Cohort (199 twin pairs and 4 singletons; 61% monozygous) and the Netherlands Twin Register (266 twin pairs and 62 singletons; 84% monozygous). Bivariate quantitative genetic modeling of the twin data showed that a majority of the phenotypic correlations between methylation levels of these CpG sites and BP could be explained by shared unique environmental rather than genetic factors, with 100% of the correlations of systolic BP with cg19693031 ( TXNIP ) and cg00716257 ( JDP2 ) determined by environmental effects acting on both systolic BP and methylation levels.

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DNA Methylation Network Estimation with Sparse Latent Gaussian Graphical Model

10.1101/367748 ◽

2018 ◽

Author(s):

Bernard Ng ◽

Sina Jafarzadeh ◽

Daniel Cole ◽

Anna Goldenberg ◽

Sara Mostafavi

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Latent Variables ◽

Latent Class ◽

Graphical Model ◽

Expression Patterns ◽

Methylation Data ◽

Gaussian Graphical Model ◽

Cpg Sites ◽

Network Estimation

AbstractInferring molecular interaction networks from genomics data is important for advancing our understanding of biological processes. Whereas considerable research effort has been placed on inferring such networks from gene expression data, network estimation from DNA methylation data has received very little attention due to the substantially higher dimensionality and complications with result interpretation for non-genic regions. To combat these challenges, we propose here an approach based on sparse latent Gaussian graphical model (SLGGM). The core idea is to perform network estimation on q latent variables as opposed to d CpG sites, with q<<d. To impose a correspondence between the latent variables and genes, we use the distance between CpG sites and transcription starting sites of the genes to generate a prior on the CpG sites’ latent class membership. We evaluate this approach on synthetic data, and show on real data that the gene network estimated from DNA methylation data significantly explains gene expression patterns in unseen datasets.

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