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

ABSTRACT: Promoter methylome and integrative transcriptome profiling identify key epigenetics-regulated genes in human HCCs

PROVIDER: PRJNA240899 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1186500_1.fastq.gz	Fastqsanger.gz
	SRR1186500_2.fastq.gz	Fastqsanger.gz
	SRR1186510_1.fastq.gz	Fastqsanger.gz
	SRR1186510_2.fastq.gz	Fastqsanger.gz
	SRR1186600_1.fastq.gz	Fastqsanger.gz

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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.

2014-07-01 | E-GEOD-55752 | biostudies-arrayexpress

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

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 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 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 larger number of samples and screened candidate genes aberrantly regulated by DNA methylation in human HCCs.

2014-07-01 | GSE55758 | GEO

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

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

Project description:This SuperSeries is composed of the SubSeries listed below.

2014-07-01 | GSE55759 | GEO

Homo sapiens

Project description:Promoter methylome and integrative transcriptome profiling identify key epigenetics-regulated genes in human HCCs [expression]

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Homo sapiens

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

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Integrative Epigenetic and Gene Expression Analysis of Renal Tumor Progression to Metastasis

Project description:Renal cell carcinoma (RCC) is among the ten most common malignancies. By far, the most common histology is clear cell (ccRCC). The Cancer Genome Atlas and other large scale sequencing studies of ccRCC have been integral to the current understanding of molecular events underlying RCC and its biology. However, these data sets have focused on primary RCC which often demonstrates indolent behavior. In contrast, metastatic disease is the major cause of mortality associated with ccRCC. However, data sets examining metastatic tumor are sparse. We therefore undertook an integrative analysis of gene expression and DNA methylome profiling of metastatic ccRCC in addition to primary RCC and normal kidney. Integrative analysis of the methylome and transcriptome identified over 30 RCC specific genes whose mRNA expression inversely correlated with promoter methylation including several known targets of hypoxia inducible factors (HIFs). Notably, genes encoding several metabolism-related proteins were identified as differentially regulated via methylation. Collectively, our data provide novel insight into biology of aggressive RCC. Furthermore, they demonstrate a clear role for epigenetics in the promotion of HIF signaling and invasive phenotypes in renal cancer.

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