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Identification of DNA methylation-independent epigenetic events underlying clear cell renal cell carcinoma

ABSTRACT: Genome-wide analysis of endogenous and exogenous methylation in human ccRCC tumor and adjacent normal tissue to determine DNA methylation and chromatin structure states in ccRCC.

ORGANISM(S): Homo sapiens

PROVIDER: GSE70303 | GEO | 2016/03/15

SECONDARY ACCESSION(S): PRJNA288277

REPOSITORIES: GEO

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Identification of DNA methylation-independent epigenetic events underlying clear cell renal cell carcinoma

Project description:Genome-wide analysis of endogenous and exogenous methylation in human ccRCC tumor and adjacent normal tissue to determine DNA methylation and chromatin structure states in ccRCC. Nuclei from the 6 patient kidney tumor and normal samples were either treated or not-treated with M.SssI enzyme, DNA was extracted and bisulfite-converted, then hybridised to the Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)

2016-03-15 | E-GEOD-70303 | biostudies-arrayexpress

Identification of DNA methylation-independent epigenetic events underlying clear cell renal cell carcinoma

Project description:Alterations in chromatin accessibility independent of DNA methylation can affect cancer-related gene expression, but are often overlooked in conventional epigenomic profiling approaches. In this study, we describe a cost-effective and computationally simple assay called AcceSssIble to simultaneously interrogate DNA methylation and chromatin accessibility alterations in primary human clear cell renal cell carcinomas (ccRCC). Our study revealed significant perturbations to the ccRCC epigenome, and identified gene expression changes that were specifically attributed to the chromatin accessibility status whether or not DNA methylation was involved. Compared to commonly mutated genes in ccRCC, such as the von Hippel-Lindau (VHL) tumor suppressor, the genes identified by AcceSssIble comprised distinct pathways and more frequently underwent epigenetic changes, suggesting that genetic and epigenetic alterations could be independent events in ccRCC. Specifically, we found unique DNA methylation-independent promoter accessibility alterations in pathways mimicking VHL deficiency. Overall, this study provides a novel approach for identifying new epigenetic-based therapeutic targets, previously undetectable by DNA methylation studies alone, that may complement current genetic-based treatment strategies. Examination of 3 different histone modifications in 2 patient tumor and adjacent normal samples.

2016-03-15 | E-GEOD-75597 | biostudies-arrayexpress

Identification of DNA methylation-independent epigenetic events underlying clear cell renal cell carcinoma

2016-03-15 | GSE75597 | GEO

Epigenome analysis of clear cell renal cell carcinoma (ccRCC) tissue versus matched normal kidney tissue

Project description:Genome wide DNA methylation profiling of clear cell renal cell carcinoma (ccRCC) tissue versus matched normal kidney tissue. TheÂ IlluminaÂ Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximatelyÂ 450,000 CpGs in tumor and adjacent normal kidney tissue samples from ccRCC patients. Samples included 46 paired fresh frozen ccRCC tumor and adjacent normal kidney tissues. Bisulphite converted DNA from the 92 samples were hybridised to the Illumina Infinium 450 Human Methylation Beadchip v1.2

2015-10-26 | E-GEOD-61441 | biostudies-arrayexpress

Epigenome analysis of clear cell renal cell carcinoma (ccRCC) tissue versus matched normal kidney tissue

Project description:Genome wide DNA methylation profiling of clear cell renal cell carcinoma (ccRCC) tissue versus matched normal kidney tissue. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in tumor and adjacent normal kidney tissue samples from ccRCC patients. Samples included 46 paired fresh frozen ccRCC tumor and adjacent normal kidney tissues.

2015-10-26 | GSE61441 | GEO

Identification of DNA Methylation-Independent Epigenetic Events Underlying Clear Cell Renal Cell Carcinoma.

Project description: Not available

| S-EPMC4873378 | biostudies-literature

Integrative genome-wide gene expression profiling of clear cell renal cell carcinoma in Czech Republic

Project description:We conducted whole-genome expression profiling on 101 pairs of ccRCC tumours and adjacent non-tumour renal tissue from Czech patients using the Illumina HumanHT-12 v4 Expression BeadChips to explore the molecular variations underlying the biological and clinical heterogeneity of ccRCC. Total RNA obtained from frozen ccRCC tumour and adjacent non-tumour renal tissue.

2013-06-03 | E-GEOD-40435 | biostudies-arrayexpress

A transcriptional metastatic signature predicts survival in clear cell renal cell carcinoma

Project description:Novel single cell technologies have paved the way for the characterization and improved biological understanding of clear cell renal cell carcinoma (ccRCC) where the focus has been mostly on the immunological compartments of the tumor microenvironment (TME). However, the identification of metastatic tumor cell clones, and the stromal compartments of TME of untreated ccRCC patients still remains to be elucidated. Here we perform single-cell RNA-sequencing on treatment naive ccRCC and adjacent normal kidney tissue.

2022-08-18 | GSE178481 | GEO

microRNAseq of clear-cell renal cell carcinoma on surgical resection specimens of untreated primary tumors in humans

Project description:We aimed to assess differences in miRNA expression profiles in transcriptomic molecular subtypes of ccRCC (Beuselinck et al, Clinical Cancer Research 2015) and to correlate miRNAs with overal survival since diagnosis of ccRCC. Sequencing was done for 129 primary ccRCC (formalin-fixed paraffin-embedded surgical resection specimens, previously untreated) and 16 normal kidney specimens. Normal kidney was obtained from the nephrectomy specimens at time of ccRCC removal, in tissue blocks containing only normal kidney (so nót the normal kidney immediately adjacent to ccRCC). The samples were sequenced in 2 major batches (2014 and 2017).

2020-07-22 | E-MTAB-9380 | biostudies-arrayexpress

Integrative genome-wide gene expression profiling of clear cell renal cell carcinoma in Czech Republic

2013-06-03 | GSE40435 | GEO

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