Novel Zinc-related Differentially Methylated Regions in leukocytes of women with and without obesity
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PROVIDER: PRJNA799048 | ENA |
REPOSITORIES: ENA
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Project description:Introduction: Nutriepigenetic markers are predictive responses associated with changes in human "surrounding" environmental conditions, which may influence metabolic diseases. Although rich in calories, Western diets could be linked with the deficiency of micronutrients, resulting in the downstream of epigenetic and metabolic effects and consequently in obesity. Zinc (Zn) is an essential nutrient associated with distinct biological roles in human health. Despite its importance in metabolic processes, little is known about the Zn-epigenetic. Thus, the present study aimed to identify the epigenetic variables associated with Zn daily ingestion (ZnDI) and serum Zinc (ZnS) levels in women with and without obesity. Materials and methods: this is a case-control, non-randomized, single-center study conducted with 21 women allocated into two groups: Control Group (CG), composed of 11 women without obesity, and Study Group (SG), composed of 10 women with obesity. Anthropometric measurements, ZnDI, and ZnS levels were evaluated. Also, the leukocyte DNA was extracted for DNA methylation analysis using the 450k Illumina BeadChips. The Epigenetic Clock was calculated by the Horvath method. The ChAMP package selected the Differentially Methylated Regions (DMRs). Results: The SG had lower ZnS levels than the CG. Moreover, in SG, the ZnS levels were negatively associated with the epigenetic age acceleration. The DMR analysis revealed 37 DMRs associated with ZnDI and ZnS levels. The DMR of the PM20D1 gene was commonly associated with ZnDI and ZnS levels and was hypomethylated in the SG. Conclusion: Our findings provide new information on Zn's modulation of DNA methylation patterns and bring new perspectives for understanding the nutriepigenetic mechanisms in obesity.
2022-01-21 | GSE193836 | GEO
Project description:IntroductionNutriepigenetic markers are predictive responses associated with changes in "surrounding" environmental conditions of humans, which may influence metabolic diseases. Although rich in calories, Western diets could be linked with the deficiency of micronutrients, resulting in the downstream of epigenetic and metabolic effects and consequently in obesity. Zinc (Zn) is an essential nutrient associated with distinct biological roles in human health. Despite the importance of Zn in metabolic processes, little is known about the relationship between Zn and epigenetic. Thus, the present study aimed to identify the epigenetic variables associated with Zn daily ingestion (ZnDI) and serum Zinc (ZnS) levels in women with and without obesity.Materials and methodsThis is a case-control, non-randomized, single-center study conducted with 21 women allocated into two groups: control group (CG), composed of 11 women without obesity, and study group (SG), composed of 10 women with obesity. Anthropometric measurements, ZnDI, and ZnS levels were evaluated. Also, leukocyte DNA was extracted for DNA methylation analysis using 450 k Illumina BeadChips. The epigenetic clock was calculated by Horvath method. The chip analysis methylation pipeline (ChAMP) package selected the differentially methylated regions (DMRs).ResultsThe SG had lower ZnS levels than the CG. Moreover, in SG, the ZnS levels were negatively associated with the epigenetic age acceleration. The DMR analysis revealed 37 DMRs associated with ZnDI and ZnS levels. The DMR of PM20D1 gene was commonly associated with ZnDI and ZnS levels and was hypomethylated in the SG.ConclusionOur findings provide new information on Zn's modulation of DNA methylation patterns and bring new perspectives for understanding the nutriepigenetic mechanisms in obesity.
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Project description:Obesity with adiposity is a common disorder in modern days, influenced by environmental factors such as eating and lifestyle habits and affecting the epigenetics of adipose-based gene regulations and metabolic pathways in colorectal cancer (CRC). We compared epigenetic changes of differentially methylated regions (DMR) of genes in colon tissues of 225 colon cancer cases (154 non-obese and 71 obese) and 15 healthy non-obese controls by accessing The Cancer Genome Atlas (TCGA) data. We applied machine-learning-based analytics including generalized regression (GR) as a confirmatory validation model to identify the factors that could contribute to DMRs impacting colon cancer to enhance prediction accuracy. We found that age was a significant predictor in obese cancer patients, both alone (p = 0.003) and interacting with hypomethylated DMRs of ZBTB46, a tumor suppressor gene (p = 0.008). DMRs of three additional genes: HIST1H3I (p = 0.001), an oncogene with a hypomethylated DMR in the promoter region; SRGAP2C (p = 0.006), a tumor suppressor gene with a hypermethylated DMR in the promoter region; and NFATC4 (p = 0.006), an adipocyte differentiating oncogene with a hypermethylated DMR in an intron region, are also significant predictors of cancer in obese patients, independent of age. The genes affected by these DMR could be potential novel biomarkers of colon cancer in obese patients for cancer prevention and progression.
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Project description:Comparison of DNA methylation levels of chromosome 18 between placentas and blood cells of pregnant women Extracted DNA from 5 cases of placental tissues and 5 cases of maternal blood cell was subjected to MeDIP (methylated DNA immunoprecipitation) and hybridized to Affymetrix GeneChip® Human Tiling 2.0R Array sets. A control without immunoprecipitation (IP) was also processed in parallel with the immunoprecipitated DNA samples. The results were validated with bisulfite sequencing and mass spectrometry-based analysis
2010-12-22 | E-GEOD-22837 | biostudies-arrayexpress
Project description:Characterization of leukocytes
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Project description:We performed a genome wide methylation scan using the Illumina HumanMethylation27 BeadChip on DNAs extracted from the leukocytes of 7 obese (BMI≥99th percentile for age and sex) and 7 lean (BMI≤10th percentile for age and sex) African American males aged 14-18 years.
2010-11-29 | GSE25301 | GEO
Project description:We here describe our independent uncovering of CARNMT1 as a protein histidine methyltransferase (HMT), and our extensive efforts on defining its substrate specificity and methylation targets. We found that recombinant CARNMT1 methylated MYLK2-derived peptide containing His-148 in vitro. The recombinant CARNMT1 methylated also several proteins in extracts from CARNMT1 KO cells, and, using protein mass spectrometry, we identified several fully methylated CARNMT1 targets, all of which were C3H zinc finger (C3H ZnF) proteins. These included the previously identified U2AF1, ZC3H15 and ZC3H18, but also the novel substrates RBM22, PPP1R10, PRR3 and RNF113A. We also identified several of the homologous methylation events in Caenorhabditis elegans and showed that they could be introduced by the nematode CARNMT in vitro.
2025-07-28 | PXD060821 | Pride
Project description:We performed a genome wide methylation scan using the Illumina HumanMethylation27 BeadChip on DNAs extracted from the leukocytes of 7 obese (BMI?99th percentile for age and sex) and 7 lean (BMI?10th percentile for age and sex) African American males aged 14-18 years. Bisulphite converted DNA from the 14 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2
2010-11-29 | E-GEOD-25301 | biostudies-arrayexpress
Project description:We sequenced 12 samples from 6 healthy women. 3 women were below 30 years of age, and the other 3 were above 70 years. For each woman, both the cecum and the sigmoid section of the colon were sequenced. The objective was to differentiate age from tumor associated hypermethylation (from a related dataset), in order to identify tumor-associated differentially methylated regions that do not change upon ageing of normal colonic mucosa.
2020-12-04 | E-MTAB-9665 | biostudies-arrayexpress