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Epigenetic heterogeneity hotspots in human liver disease progression [MethylationEPIC Beadchip]

ABSTRACT: Epigenetic heterogeneity hotspots in human liver disease progression [MethylationEPIC Beadchip]

PROVIDER: PRJNA1099241 | ENA |

REPOSITORIES: ENA

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Epigenetic heterogeneity hotspots in human liver disease progression [MethylationEPIC Beadchip]

Project description:Disruption of the epigenome is a hallmark of human disease including liver cirrhosis and hepatocellular carcinoma (HCC). While genetic heterogeneity is an established effector of pathologic phenotypes, epigenetic heterogeneity is less well understood. Environmental exposures including hepatitis C viral (HCV) infection and metabolic syndrome alter the liver-specific DNA methylation landscape and influence the onset of liver cancer. Given that currently available treatments are unable to target the most frequently mutated genes in HCC, there is an unmet need for novel therapeutic strategies to prevent or reverse hepatic tumorigenesis, which the epigenome may provide. We performed genome-wide profiling of DNA methylation, copy number, and gene expression landscapes from multiple liver regions from 31 patients with liver disease to examine their crosstalk and define the individual and combinatorial contribution of these processes to liver disease progression. We identify epigenetic heterogeneity hotspots that are conserved across patients. Elevated epigenetic heterogeneity associates with increases in gene expression heterogeneity. Cirrhotic regions comprise two distinct cohorts, one exclusively epigenetic, and a second where epigenetic and copy number variations collaborate. Epigenetic heterogeneity hotspots are enriched for genes central to liver function (e.g., HNF1A) and known tumor suppressors (e.g., RASSF1A). These hotspots encompass genes including ACSL1, ACSL5, MAT1A, and ELFN1, which have phenotypic effects in cell line functional screens, supporting their relevance to hepatocarcinogenesis. Substantial epigenetic heterogeneity arises early in liver disease development, targeting key pathways in the progression and initiation of both cirrhosis and HCC. Integration of epigenetic and transcriptional heterogeneity unveils putative epigenetic regulators of hepatocarcinogenesis.

2024-07-30 | GSE263787 | GEO

Evaluating The Infinium Human MethylationEPIC v2 BeadChip

Project description:Evaluating The Infinium Human MethylationEPIC v2 BeadChip

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Epigenetic heterogeneity hotspots in human liver disease progression [RNA-seq]

2024-07-30 | GSE263786 | GEO

Epigenetic heterogeneity hotspots in human liver disease progression [RNA-seq]

Project description:Epigenetic heterogeneity hotspots in human liver disease progression [RNA-seq]

| PRJNA1099239 | ENA

Illumina Infinium MethylationEPIC BeadChip (850k) analysis of growing teratoma tissues

Project description:Illumina Infinium MethylationEPIC BeadChip (850k) array analysis of DNA methylation of 12 different growing teratoma tissues. Samples were subgrouped based on growth speed into GTSslow to GTSrapid (see corresponding publication).

2024-04-28 | GSE240091 | GEO

Evaluating The Infinium Human MethylationEPIC v2 BeadChip

Project description:We conducted a comprehensive evaluation of the updated Infinium MethylationEPIC v2 BeadChip (EPICv2). Our evaluation revealed that EPICv2 offers significant improvements over its predecessors, including expanded enhancer coverage, applicability to diverse ancestry groups, support for low-input DNA down to one nanogram, coverage of existing epigenetic clocks, cell type deconvolution panels, and human trait associations, while maintaining accuracy and reproducibility.

2023-07-04 | GSE228820 | GEO

Illumina Infinium MethylationEPIC BeadChip (850k) analysis of growing teratoma tissues

Project description:Illumina Infinium MethylationEPIC BeadChip (850k) analysis of growing teratoma tissues

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Illumina Infinium MethylationEPIC BeadChip (850k) data of germ cell tumor-related somatic-type maligancies

Project description:Illumina Infinium MethylationEPIC BeadChip (850k) array analysis of DNA methylation of germ cell tumor related somati-type malignancies (STM), i. e. adenocarcinomas and rhabdomyosarcomas. As controls, yolk-sac tumors and teratoma without STM population were included.

2023-05-23 | GSE219033 | GEO

Distinguishing active versus passive DNA demethylation using Illumina MethylationEPIC BeadChip microarrays

Project description:Distinguishing active versus passive DNA demethylation using Illumina MethylationEPIC BeadChip microarrays

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Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling [MethylationEPIC]

Project description:We performed a critical evaluation of the new Infinium MethylationEPIC BeadChip microarray. EPIC covers over 850,000 CpG sites, including >90% of the CpGs from the HumanMethylation450 (HM450) BeadChip and an additional 413,743 CpGs. Even though the additional probes improve the coverage of regulatory elements, including 58% of FANTOM5 enhancers, only 7% distal and 27% proximal ENCODE regulatory elements are represented. Detailed comparisons of regulatory elements from EPIC and whole-genome bisulphite sequencing data (WGBS) show that a single EPIC probe is not always informative for those distal regulatory elements showing variable methylation across the region. However, overall data from the EPIC array at single loci are highly reproducible across technical and biological replicates and demonstrate high correlation with HM450 and WGBS data. We show that the HM450 and EPIC arrays distinguish differentially methylated probes, but the absolute agreement depends on the threshold set for each platform.

2016-09-12 | GSE86831 | GEO

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