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Homo sapiens

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

PROVIDER: PRJNA304737 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2969510.fastq.gz	Fastqsanger.gz
	SRR2969520.fastq.gz	Fastqsanger.gz
	SRR2969511.fastq.gz	Fastqsanger.gz
	SRR2969521.fastq.gz	Fastqsanger.gz
	SRR2969512.fastq.gz	Fastqsanger.gz

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Homo sapiens

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

| PRJNA288277 | ENA

Loss of 5-hydroxymethylcytosine is linked to gene body hypermethylation in kidney cancer

Project description:Aberrant DNA methylation is common in cancer. To associate DNA methylation with gene function, we performed RNAseq upon tumor tissue and matched normal tissues of two ccRCC (clear cell renal cell carcinoma) patients. To quantify 5mC and 5hmC level in each CG site at genome-wide level, we performed BS-seq and TAB-seq upon tumor tissue and matched normal tissues of two ccRCC (clear cell renal cell carcinoma) patients, respectively. mRNA profiles of tumor and matched normal tissues from two ccRCC patients were generated by deep sequencing, using Hiseq 2000. Single-nucleotide-resolution, whole-genome, 5mC and 5hmC profiles of tumor and matched normal tissues from two ccRCC (clear cell renal cell carcinoma) patients were generated by deep sequencing, using Hiseq 2000.

2016-02-29 | E-GEOD-63183 | 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

Understanding the biological processes of clear cell renal carcinoma carcinogenesis: an integrative multi-omics approach.

Project description:Multi-Omics analysis to gain novel insights into clear cell renal carcinoma aetiology and progression. The DNA methylation data of 121 clear clear renal carcinoma (ccRCC) were integrated with WGS and transcriptomic data using Multi-Omics Factor Analysis (MOFA) to detect the inter-patient variations related to aetiological and disease progression related factors.

2024-06-07 | GSE269180 | GEO

Loss of 5-hydroxymethylcytosine is linked to gene body hypermethylation in kidney cancer

2016-02-29 | GSE63183 | GEO

Homo sapiens

Project description:Methylation microarray data of human clear cell renal cell carcinoma

| PRJNA352797 | ENA

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

2016-03-15 | GSE75597 | GEO

Gene expression analysis of collecting duct carcinoma

Project description:We performed a transcriptomic analysis in a cohort of 6 Collecting Duct Carcinoma, 5 Clear Cell Renal Cell Carcinoma and 4 non-matched normal renal tissues to unravel the underlying biological and molecular determinants and to identifiy specific genes and pathways of this rare tumor type.

2021-07-13 | GSE153965 | GEO

Profiling of chromosomal alterations in renal cell carcinoma using high-density single nucleotide polymorphism arrays

Project description:We applied Illumina’s 317K high-density SNP-arrays to profile chromosomal aberrations in clear cell renal cell carcinoma (ccRCC) from 80 patients and analyzed the association of LOH/amplification events with clinicopathological characteristics

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The deubiquitylating enzyme USP35 restricts regulated cell death to promote survival of renal clear cell carcinoma

Project description:The ubiquitin proteasome system governs a wide spectrum of cellular events and offers therapeutic opportunities for pharmacological intervention in cancer treatment. Renal clear cell carcinoma represents the predominant histological subtype and accounts for the majority of cancer death related to kidney malignancies. Through a systematic survey in the association of human ubiquitin-specific proteases with patient prognosis of renal clear cell carcinoma and subsequent phenotypic validation, we uncovered the tumor-promoting role of USP35. Biochemical characterizations confirmed the stabilizing effects of USP35 towards multiple members of the IAP family in an enzymatic activity-dependent manner. USP35 silencing led to reduced expression levels of IAP proteins, which were accompanied with increased cellular apoptosis. Further transcriptomic analysis revealed that USP35 knockdown altered expression levels of NRF2 downstream transcripts, which were conferred by compromised NRF2 abundance. USP35 functions to maintain NRF2 levels by catalyzing its deubiquitylation and thus antagonizing degradation. NRF2 reduction imposed by USP35 silencing rendered renal clear cell carcinoma cells increased sensitivity to ferroptosis induction. Finally, induced USP35 knockdown markedly attenuated xenograft formation of renal clear cell carcinoma in nude mice. Hence, our findings identify a number of USP35 substrates and reveal the protecting role of USP35 against both apoptosis and ferroptosis in renal clear cell carcinoma.

2023-06-17 | GSE216154 | GEO

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