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Altered Hydroxymethylation is seen at regulatory regions in pancreatic cancer and regulates oncogenic pathways [ATAC-seq]

ABSTRACT: Transcriptional deregulation of oncogenic pathways is a hallmark of cancer, and can be due to epigenetic alterations. 5-hydroxymethylcytosine is a recently discovered epigenetic modification that has not been studied in pancreatic cancer. Genome-wide analysis of 5-hmC enriched loci with hmC-seal was conducted in low-passage pancreatic cancer cell lines and primary patient-derived xenografts and revealed strikingly altered patterns in neoplastic tissues. Differentially hydroxymethylated regions preferentially affected regulatory regions of the genome, specifically overlapping with known H3K4me1 enhancers. Furthermore, base pair resolution analysis of methylation and hydroxymethylation with oxidative bisulfite sequencing was conducted and correlated with chromatin accessibility by ATAC-seq in pancreatic cancer and control samples. 5hmC was specifically enriched at open regions of chromatin and gain of 5-hmC was correlated with upregulation of the cognate transcripts, including many oncogenic pathways implicated in pancreatic neoplasia, such as myc, KRAS, VEGF and BRD4. Specifically, BRD4 was overexpressed and acquired 5hmC at enhancer regions in majority of neoplastic samples. Functionally, acquisition of 5hmC at BRD4 promoter regulated increase in transcript expression. Furthermore, blockade of BRD4 inhibited pancreatic cancer growth in vivo. In summary, redistribution of 5-hmC and preferential enrichment at oncogenic enhancers is a novel regulatory mechanism in human cancer.

ORGANISM(S): Homo sapiens

PROVIDER: GSE97008 | GEO | 2017/09/14

SECONDARY ACCESSION(S): PRJNA380396

REPOSITORIES: GEO

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Altered Hydroxymethylation is seen at regulatory regions in pancreatic cancer and regulates oncogenic pathways [MeDIP-seq]

Project description:Transcriptional deregulation of oncogenic pathways is a hallmark of cancer, and can be due to epigenetic alterations. 5-hydroxymethylcytosine is a recently discovered epigenetic modification that has not been studied in pancreatic cancer. Genome-wide analysis of 5-hmC enriched loci with hmC-seal was conducted in low-passage pancreatic cancer cell lines and primary patient-derived xenografts and revealed strikingly altered patterns in neoplastic tissues. Differentially hydroxymethylated regions preferentially affected regulatory regions of the genome, specifically overlapping with known H3K4me1 enhancers. Furthermore, base pair resolution analysis of methylation and hydroxymethylation with oxidative bisulfite sequencing was conducted and correlated with chromatin accessibility by ATAC-seq in pancreatic cancer and control samples. 5hmC was specifically enriched at open regions of chromatin and gain of 5-hmC was correlated with upregulation of the cognate transcripts, including many oncogenic pathways implicated in pancreatic neoplasia, such as myc, KRAS, VEGF and BRD4. Specifically, BRD4 was overexpressed and acquired 5hmC at enhancer regions in majority of neoplastic samples. Functionally, acquisition of 5hmC at BRD4 promoter regulated increase in transcript expression. Furthermore, blockade of BRD4 inhibited pancreatic cancer growth in vivo. In summary, redistribution of 5-hmC and preferential enrichment at oncogenic enhancers is a novel regulatory mechanism in human cancer.

2017-09-14 | GSE97014 | GEO

Altered Hydroxymethylation is seen at regulatory regions in pancreatic cancer and regulates oncogenic pathways [RNA-seq]

2017-09-14 | GSE97003 | GEO

Altered patterns of hydroxymethylation regulate oncogenic pathways in pancreatic cancer

Project description:Transcriptional deregulation of oncogenic pathways is a hallmark of cancer, and can be due to epigenetic alterations. 5-hydroxymethylcytosine is a recently discovered epigenetic modification that has not been studied in pancreatic cancer. Genome-wide analysis of 5-hmC enriched loci was conducted in low-passage pancreatic cancer cell lines and primary patient-derived xenografts and revealed strikingly altered patterns in neoplastic tissues. Differentially hydroxymethylated regions preferentially affected regulatory regions of the genome, specifically overlapping with H3K4me1 enhancers. Gain of 5-hmC was correlated with upregulation of the cognate transcripts, including many oncogenic pathways implicated in pancreatic neoplasia. Specifically, BRD4 was overexpressed and acquired 5hmC at enhancer regions in majority of neoplastic samples. Functionally, acquisition of 5hmC at BRD4 promoter regulated increase in transcript expression. Furthermore, blockade of BRD4 inhibited pancreatic cancer growth in vivo. In summary, redistribution of 5-hmC and preferential enrichment at oncogenic enhancers is a novel regulatory mechanism in human cancer. Genome-wide analysis of 5-hmC enriched loci was conducted in low-passage pancreatic cancer cell lines and primary patient-derived xenografts

2016-08-06 | E-GEOD-71839 | biostudies-arrayexpress

Altered patterns of hydroxymethylation regulate oncogenic pathways in pancreatic cancer

Project description:Transcriptional deregulation of oncogenic pathways is a hallmark of cancer, and can be due to epigenetic alterations. 5-hydroxymethylcytosine is a recently discovered epigenetic modification that has not been studied in pancreatic cancer. Genome-wide analysis of 5-hmC enriched loci was conducted in low-passage pancreatic cancer cell lines and primary patient-derived xenografts and revealed strikingly altered patterns in neoplastic tissues. Differentially hydroxymethylated regions preferentially affected regulatory regions of the genome, specifically overlapping with H3K4me1 enhancers. Gain of 5-hmC was correlated with upregulation of the cognate transcripts, including many oncogenic pathways implicated in pancreatic neoplasia. Specifically, BRD4 was overexpressed and acquired 5hmC at enhancer regions in majority of neoplastic samples. Functionally, acquisition of 5hmC at BRD4 promoter regulated increase in transcript expression. Furthermore, blockade of BRD4 inhibited pancreatic cancer growth in vivo. In summary, redistribution of 5-hmC and preferential enrichment at oncogenic enhancers is a novel regulatory mechanism in human cancer.

2016-08-06 | GSE71839 | GEO

Genome wide hydroxymethylation tested using the HELP-GT assay shows redistribution in cancer

Project description:Background: 5-hydroxymethylcytosine (5-hmC) is a recently discovered epigenetic modification that is altered in cancers. Genome wide assays for 5-hmC determination are needed as many of the techniques commonly used to assay 5-methylcytosine (5-mC), including conventional methyl-sensitive restriction digest and bisulfite sequencing, are incapable of distinguishing between 5-mC and 5-hmC. Results: Glycosylation of 5-hmC residues by beta-Glucosyl Transferase (beta-GT) can make CCGG residues insensitive to digestion by MspI. We used this premise to modify the HELP-tagging assay to identify both 5-mC and 5-hmC loci in the genome. Comparison of sequencing libraries after HpaII, MspI and MspI+ beta-GT conversion resulted in locus specific 5-mC and 5-hmC determination. A custom bioinformatics pipeline was created to identify 5-hmC sites that were validated at global level by LS-MS and the locus specific level by qRT-PCR of 5-hmC pulldown DNA. Hydroxymethylation at both promoter and intragenic locations correlated positively with gene expression. Analysis of pancreatic cancer samples revealed striking redistribution of 5-hmC sites in cancer cells and demonstrated enrichment of this modification at many oncogenic promoters such as GATA6. Conclusions: The HELP-GT assay allows a high resolution, simultaneous determination of 5-hmC and 5-mC loci from small amounts of DNA with the utilisation of modest sequencing resources. Redistribution of 5-hmC seen in cancer highlights the importance of examining this modification in conjugation with conventional methylome analysis. We did methylation and hydroxymethylation tests for one control and two pancreatic cancer cases

2013-07-30 | E-GEOD-42723 | biostudies-arrayexpress

Altered Hydroxymethylation is seen at regulatory regions in pancreatic cancer and regulates oncogenic pathways

Project description:Altered Hydroxymethylation is seen at regulatory regions in pancreatic cancer and regulates oncogenic pathways

| PRJNA380406 | ENA

Global distribution of DNA hydroxymethylation and DNA methylation in chronic lymphocytic leukemia

Project description:We studied global distribution of hydroxymethylation (5hmC) and DNA methylation (5mC) in during normal B-cell development and CLL maturation. To derive disease-specific epigenetic changes we have compared CLL subgroups to their corresponding cell of origin. Our data showed that naïve B-cells, compared to non-class switched and class switched memory B-cells, had higher levels of 5-hmC and 5-mC. By comparing with ChIP sequencing data of H3K27Ac and H3K4me1 modifications of CLL samples with 5hmC and 5mC levels, we observed an increase of 5-hmC at overall gene body regions, CpG island shores and regulatory elements. Comparing 5-hmC distribution with RNA sequencing we showed that genes with higher transcriptional activity had higher 5-hmC and vice versa. Thus, our study suggests that the global loss of 5-hmC levels, with significant increase at gene regulatory regions, constitute a novel hallmark of CLL pathogenesis.

2019-01-23 | GSE113386 | GEO

IP of 5-hydroxymethylcytosine (5-hmC) enriched DNA fragments from control and PB treated mouse livers

Project description:5-hmC is a novel epigenetic mark derived from oxidation of methylcytosine. Phenobarbital (PB) is a well studied non-genotoxic carcinogen with roles in epigenetic perturbation. We profile 5hmC in both control mouse livers as well as in the livers of 28 day PB treated mice. 5hmC is largely found to reside in the bodies of active genes and promoter levels are perturbed upon PB induced gene activation events. 5-hmC is enriched in the bodies of active genes as well as a subset of TSS regions associated with transcriptional silencing. Upon PB exposire a handfull of genes are induced which reveal increases in promoter 5hmC levels comparison of 5hmC profiles in 5 control and 5 PB exposed mouse livers

2012-09-12 | E-GEOD-40537 | biostudies-arrayexpress

Alpha-ketoglutarate links p53 to cell fate during tumor suppression

Project description:The tumor suppressor p53 is mutated in the majority of human cancers, including pancreatic ductal adenocarcinoma (PDAC)1,2. Wild-type p53 accumulates in response to cellular stress and acts to regulate the expression of genes that influence cell fate and constrain tumorigenesis2. p53 also can modulate cellular metabolism3, though it remains unclear how the metabolic effects of p53 influence tumor suppression or whether the metabolic consequences of p53 loss play a role in disease maintenance. Here, we show that restoring endogenous p53 function in cancer cells derived from a mouse model of PDAC driven by oncogenic Kras and a regulatable p53 short hairpin RNA (shRNA) rewires glucose and glutamine metabolism to support the accumulation of the metabolite alpha-ketoglutarate, an obligate substrate for several enzymes that regulate chromatin methylation. p53 restoration induces transcriptional programs characteristic of pre-neoplastic differentiation, an effect that can be partially recapitulated by addition of cell permeable alpha-ketoglutarate. Consequently, enforcing alpha-ketoglutarate accumulation in p53 deficient cells by inhibiting expression of oxoglutarate dehydrogenase (Ogdh), the enzyme that consumes alpha-ketoglutarate in the tricarboxylic acid cycle, reduces tumor-initiating capacity and promotes tumor differentiation in vivo. In both mouse and human pancreatic cancer, decreasing levels of the alpha-ketoglutarate-dependent chromatin modification 5-hydroxymethylcytosine (5hmC) marks progression from prenoplastic to de-differentiated malignant lesions. p53 restoration or Ogdh suppression promotes accumulation of 5hmC specifically in differentiated tumor cells in vivo. Together, these results nominate alpha-ketoglutarate as an effector of p53-mediated tumor suppression that promotes pre-neoplastic differentiation and suppresses malignant progression.

2019-09-09 | GSE114263 | GEO

A highly sensitive and robust method for genome-wide 5hmC profiling of rare cell populations

Project description:Investigations of 5-hydroxymethylcytosine (5hmC) in biologically and clinically samples and models with low cell numbers have been hampered by the low sensitivity and reproducibility using current 5hmC mapping approaches. Here, we develop a selective 5hmC chemical labeling approach using tagmentation-based library preparation in order to profile nanogram levels of 5hmC isolated from ~1,000 cells (nano-hmC-Seal). Using this technology, we profiled the dynamics of 5hmC across different stages of mouse hematopoietic differentiation. Additionally, applying nano-hmC-Seal to the hematopoietic multipotent progenitor cells in an acute myeloid leukemia (AML) mouse model, we identified leukemia-specific, differentially hydroxymethylated regions that harbor previously reported and as-yet-unidentified functionally relevant factors. The change of 5hmC patterns in AML strongly correlates with the altered gene expression on a global scale. Together, our new approach offers a highly sensitive and robust method to study and detect DNA methylation dynamics from in vivo model and clinical samples. Selective 5hmC chemical labeling approach using tagmentation-based library preparation in order to profile nanogram levels of 5hmC isolated from ~1,000 cells

2016-09-01 | E-GEOD-77967 | biostudies-arrayexpress

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