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Epigenome-wide DNA methylation analysis in inflammatory breast cancer

ABSTRACT: Epigenome-wide DNA methylation analysis in inflammatory breast cancer

PROVIDER: PRJNA997959 | ENA |

REPOSITORIES: ENA

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Epigenome-wide DNA methylation analysis in inflammatory breast cancer

Project description:Genome-wide DNA methylation analysis (Infinium Human Methylation EPIC BeadChip platform, Illumina) performed in 24 IBCs and six normal breast tissues.

2024-08-27 | GSE238092 | GEO

Epigenome-wide DNA methylation profiling in CBMCs

Project description:Epigenome-wide DNA methylation profiling in CBMCs

| PRJNA788914 | ENA

An Epigenome-Wide Analysis of Socioeconomic Position and Tumor DNA Methylation in Breast Cancer Patients

Project description:Background: Disadvantaged socioeconomic position (SEP), including lower educational attainment and household income, may influence cancer risk and outcomes. We hypothesized that DNA methylation could function as an intermediary epigenetic mechanism that internalizes and reflects the biological impact of SEP. Methods: Based on tumor DNA methylation data from the Illumina 450K array from 694 breast cancer patients in the Women’s Circle of Health Study, we conducted an epigenome-wide analysis in relation to educational attainment and household income. Functional impact of the identified CpG sites was explored in silico using data from publicly available databases. Results: We identified 25 CpG sites associated with household income at an array-wide significance level, but none with educational attainment. Two of the top CpG sites, cg00452016 and cg01667837, were in promoter regions of NNT and GPR37, respectively, with multiple epigenetic regulatory features identified in each region. NNT is involved in -adrenergic stress signaling and inflammatory responses, whereas GPR37 is involved in neurological and immune responses. For both loci, gene expression was inversely correlated to the levels of DNA methylation. The associations were consistent between Black and White women, and did not differ by tumor estrogen receptor (ER) status. Conclusions: In a large breast cancer patient population, we discovered evidence of the significant biological impact of household income on the tumor DNA methylome, including genes in the -adrenergic stress and immune response pathways. Our findings support biological effects of socioeconomic status on tumor tissues which might be relevant to cancer development and progression.

2023-03-31 | GSE226569 | GEO

Integrative Epigenome-Wide Analysis Shows That DNA Methylation May Mediate Genetic Risk In Inflammatory Bowel Disease [Cells, Methylation profiling]

Project description:Epigenetic alterations may provide important insights into gene-environment interaction in inflammatory bowel disease (IBD). Here we observe epigenome-wide DNA methylation differences in 240 newly-diagnosed IBD cases and 190 controls. These include 439 differentially methylated positions (DMPs) and 5 differentially methylated regions (DMRs), which we study in detail using whole genome bisulphite sequencing. We replicate the top DMP (RPS6KA2) and DMRs (VMP1, ITGB2, TXK) in an independent cohort. Using paired genetic and epigenetic data, we delineate methylation quantitative trait loci; VMP1/microRNA-21 methylation associates with two genetic polymorphisms in linkage disequilibrium with a known IBD susceptibility variant. Separated cell data highlight the cell type of origin of epigenetic signals seen in whole blood; IBD-associated hypermethylation within the TXK gene transcription start-sitepromoter region negatively correlates with gene expression in whole blood and CD8+ T-cells, but not other cell types. Thus, site-specific DNA methylation changes in IBD are relatedrelate to underlying genotype and associate with cell-specific alteration in gene expression.

2016-11-13 | GSE87640 | GEO

Hormone Therapy Use and Breast Tissue DNA Methylation: Analysis of Epigenome Wide Data from the Normal Breast Study

Project description:Hormone Therapy Use and Breast Tissue DNA Methylation: Analysis of Epigenome Wide Data from the Normal Breast Study

| PRJNA422860 | ENA

Integrative Epigenome-Wide Analysis Shows That DNA Methylation May Mediate Genetic Risk In Inflammatory Bowel Disease [Whole blood, Methylation profiling]

2016-11-13 | GSE87648 | GEO

An Epigenome-Wide Analysis of Socioeconomic Position and Tumor DNA Methylation in Breast Cancer Patients

Project description:An Epigenome-Wide Analysis of Socioeconomic Position and Tumor DNA Methylation in Breast Cancer Patients

| PRJNA940716 | ENA

Integrative Epigenome-Wide Analysis Shows That DNA Methylation May Mediate Genetic Risk In Inflammatory Bowel Disease

Project description:Integrative Epigenome-Wide Analysis Shows That DNA Methylation May Mediate Genetic Risk In Inflammatory Bowel Disease

| PRJNA345569 | ENA

Integrative Epigenome-Wide Analysis Shows That DNA Methylation May Mediate Genetic Risk In Inflammatory Bowel Disease [Expression profiling]

2016-11-13 | GSE86434 | GEO

Hormone Therapy Use and Breast Tissue DNA Methylation: Analysis of Epigenome Wide Data from the Normal Breast Study

Project description:Genome wide DNA methylation profiling of fresh frozen, histologically normal-appearing breast tissue from the Normal Breast Study (NBS). The Illumina HumanMethylation450 BeadChip was used to obtain DNA methylation profiles for 90 samples, including “current”, “former” and never users of HRT.

2017-12-19 | GSE108213 | GEO

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