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DNA methylation data of tumor and non-tumor liver tissues from Peruvian patients with hepatocellular carcinoma (HCC)

ABSTRACT: A large fraction of HCC in Peru arises in younger, non-cirrhotic patients. Global DNA methylation analysis of the HCC and non-tumor liver (NTL) tissues demostrate a profound overhaul of the developmental DNA methylation programme culminating in an global hyper-methylated pattern in HCC. We used microarrays to compare global DNA methylation between tumor and non-tumor liver tissues and identified CpGs and ontologies that are distinctively differentially methylated between subsets.

ORGANISM(S): Homo sapiens

PROVIDER: GSE136380 | GEO | 2021/01/31

REPOSITORIES: GEO

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DNA methylation data of tumor and non-tumor liver (NTL) tissues from Peruvian patients with hepatocellular carcinoma (HCC).

Project description:A large fraction of HCC in Peru arises in younger, non-cirrhotic patients. Global DNA methylation analysis of the HCC and non-tumor liver (NTL) tissues demostrate a profound overhaul of the developmental DNA methylation programme culminating in an global hyper-methylated pattern in HCC. We used microarrays to compare global DNA methylation between tumor and non-tumor liver tissues and identified CpGs and ontologies that are distinctively differentially methylated between subsets.

2021-01-31 | GSE136319 | GEO

DNA hydroxy-methylation data of tumor and non-tumor liver (NTL) tissues from Peruvian patients with hepatocellular carcinoma (HCC)

Project description:A large fraction of HCC in Peru arises in younger, non-cirrhotic patients. Global DNA hydroxy-methylation analysis of the HCC and NTL tissues demonstrate that hydroxy-methylation conversion interplays with gene expression to enact cell fate determination and cancer cell reprogramming. We used microarrays to identify hydroxy-methylated CpGs by comparison to Gene Expression Omnibus (GEO) series GSE136319 and GSE136380.

2021-01-31 | GSE136583 | GEO

Expression data of tumor and non-tumor liver tissues from Peruvian patients with hepatocellular carcinoma (HCC)

Project description:A large fraction of HCC in Peru arises in younger, non-cirrhotic patients. Transcriptomic analysis of the HCC and non-tumor liver (NTL) tissues highlights a divergent gene expression profile that coincides with Amerind haplogrouping. This metagene is also associated with a peculiar molecular signature that does not conform with the current molecular classifications of HCCs. We used microarrays to compare gene expression between tumors and non-tumor counter parts in order to identify genes and ontologies that are differentially expressed.

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DNA methylation data of tumor and non-tumor liver (NTL) tissues from Peruvian patients with hepatocellular carcinoma (HCC).

Project description:DNA methylation data of tumor and non-tumor liver (NTL) tissues from Peruvian patients with hepatocellular carcinoma (HCC).

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DNA hydroxy-methylation data of tumor and non-tumor liver (NTL) tissues from Peruvian patients with hepatocellular carcinoma (HCC)

Project description:DNA hydroxy-methylation data of tumor and non-tumor liver (NTL) tissues from Peruvian patients with hepatocellular carcinoma (HCC)

| PRJNA562836 | ENA

Expression data in non-tumor liver tissues from Peruvian patients with hepatocellular carcinoma.

Project description:Most hepatocellular carcinomas in younger patients from Peru arise from non-cirrhotic livers. Histological examination of the non-tumor liver tissues highlights the presence of clear cell foci in a significant fraction of Peruvian patients with hepatocellular carcinoma. We used microarrays to compare gene expression between non-tumor liver tissues with and without clear cell foci and identified ontologies that are distinctively differentially expressed between subsets.

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Promoter methylome and integrative transcriptome profiling identify key epigenetics-regulated genes in human HCCs [methylation]

Project description:Hepatocellular carcinoma (HCC) is one of the most common and lethal cancers worldwide and has a poor prognosis. Promoters represent an essential regulatory element of gene transcription in the human genome. In order to understand the promoter methylation in relation with gene transcription in HCCs, we applied a liquid hybridization capture-based bisulfite sequencing (LHC-BS) approach to examine the promoter methylome of HCCs, for which we customized 150,407 capture probes and enabled coverage of 91.8% of the RefSeq gene promoters within the human genome. We found the differential promoter DNA methylation between HCCs and peripheral normal tissues. Then we integrated promoter methylomic and transcriptomic profiling and described gene expression and regulation in HCCs. Lastly, we validated the key genes in a larger number of samples and screened candidate genes aberrantly regulated by DNA methylation in human HCCs. Capture-based whole genome promoter bisulfite-seq for 8 pairs of HCC tumor and non-tumor liver (NTL) samples.

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Integrated analyses of DNA methylation and hydroxymethylation reveal tumor suppressive roles of ECM1, ATF5 and EOMES in human hepatocellular carcinoma

Project description:The newly discovered 5-hydroxymethylcytosine (5hmC) may complicate previous observations of abnormal cytosine methylation statuses used for the identification of new tumor suppressor gene candidates relevant to human hepatocarcinogenesis. The simultaneous detection of 5mC and 5hmC will stimulate the discovery of aberrantly methylated genes with increased accuracy in human hepatocellular carcinoma (HCC). Here, we performed a newly developed single-base high-throughput sequencing approach (hydroxymethylation and methylation Sensitive Tag sequencing, HMST-seq) to synchronously measure these two modifications in HCC samples. After identifying the differentially methylated and hydroxymethylated genes in HCC, we integrated the DNA copy-number alterations as determined using array-based comparative genomic hybridization (aCGH) data with gene expression to identify genes potentially silenced by promoter hypermethylation. As a result, we report a high enrichment of genes with epigenetic aberrations in cancer signaling pathways. Six genes were selected as tumor suppressor gene (TSG) candidates, among which, ECM1, ATF5 and EOMES were confirmed to have potential anti-cancer function via siRNA experiments. To fully examine 5mC and 5hmC status in HCC, we used a newly developed single-base high-throughput sequencing approach (hydroxymethylation and methylation sensitive tag sequencing, HMST-seq) to synchronously measure these two modifications in HCC samples and their adjacent non-cancerous liver tissues (non-HCCs).

2014-09-01 | E-GEOD-54141 | biostudies-arrayexpress

DNA methylation data of tumor and non-tumor liver tissues from Peruvian patients with hepatocellular carcinoma (HCC)

Project description:DNA methylation data of tumor and non-tumor liver tissues from Peruvian patients with hepatocellular carcinoma (HCC)

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Genome-wide promoter DNA Methylation Profiling of Hepatocellular Carcinomas Arising Either Spontaneously or due to Chronic Exposure to Ginkgo biloba Extract (GBE) in B6C3F1/N Mice [Methylation]

Project description:Epigenetic modifications, such as DNA methylation, play an important role in carcinogenesis. In a recent NTP study, chronic exposure of B6C3F1/N mice to Ginkgo biloba extract (GBE) resulted in a high incidence of hepatocellular carcinomas (HCC). Genome-wide promoter methylation profiling on GBE-exposed HCC (2000 mg/kg group), spontaneous HCC (vehicle-control group) and age-matched vehicle control liver was performed to identify differentially methylated genes in GBE-exposed HCC and spontaneous HCC. DNA methylation alterations were correlated to the corresponding global gene expression changes to identify differentially methylated promoter regions of relevant cancer genes altered in GBE-exposed HCC compared to spontaneous HCC.

2020-01-01 | GSE132577 | GEO

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