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Profiling chromatin accessible regions in Merkel cell carcinoma cells

ABSTRACT: Profiling chromatin accessible regions in Merkel cell carcinoma cells

PROVIDER: PRJNA590024 | ENA |

REPOSITORIES: ENA

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Profiling chromatin accessible regions in Merkel cell carcinoma cells

Project description:Merkel cell carcinoma (MCC) is an aggressive neuroendocrine cancer of the skin, caused by either excessive UV damage or integration of the Merkel cell polyomavirus (MCV) genome. Here, we report that virally encoded MCV small T antigen (ST) establishes dependence on the LSD1 transcriptional repressor. Inhibition of LSD1 reduces growth of MCV-positive MCC and suppresses ST’s transformation capacity in vitro and in vivo. To define the mechanism of LSD1 inhibition in MCC, we performed a CRISPR loss-of-function library screen. We found that deletion of components of the non-canonical (ncBAF) chromatin remodeler complex confers resistance to LSD1 inhibitors and that LSD1 and ncBAF antagonistically regulate an overlapping set of genes involved in neuron differentiation. Our work provides mechanistic insight into the dependence of MCC on LSD1 and the role of ncBAF as a tumor suppressor in cancer.

2020-02-16 | GSE140505 | GEO

Comparative Transcriptional Profiling of human Merkel cells and Merkel Cell Carcinoma

Project description:Merkel cell carcinoma is supposed to be derived from Merkel cells after infection by Merkel cell polyomavirus (MCV) and other poorly known events. A transcriptional profiling with cDNA microarrays was performed on cells from MCV+ Merkel cell carcinomas and isolated normal Merkel cells. This microarray revealed numerous significantly upregulated genes and down-regulated genes. The extensive list of genes identified in these experiments provides a large body of potentially valuable information of Merkel cell carcinoma carcinogenesis and could represent a source of potential targets for cancer therapy. Two-conditions experiment, MCV vs Normal Merkel Cell. Biological replicates : 4 MCV (Cy5), 1 control = pool of Normal Merkel cells from 3 liftings

2014-01-01 | E-GEOD-50434 | biostudies-arrayexpress

Comparative Transcriptional Profiling of Human Merkel cells and Merkel Cell Carcinoma

Project description:Merkel cell carcinoma is supposed to be derived from Merkel cells after infection by Merkel cell polyomavirus (MCPyV) and other poorly known events. A transcriptional profiling with cDNA microarrays was performed on cells from MCPyV(+) Merkel cell carcinomas and isolated normal Merkel cells. This microarray revealed numerous significantly upregulated genes and downregulated genes. The extensive list of genes identified in these experiments provides a large body of potentially valuable information of Merkel cell carcinoma carcinogenesis and could represent a source of potential targets for cancer therapy.

2014-01-01 | GSE50434 | GEO

Effect of NKD1, NKD2 and O2 on Chromatin Accessible Regions

Project description:Effect of NKD1, NKD2 and O2 on Chromatin Accessible Regions

| PRJNA885167 | ENA

Array Comparative Genomic Hybridization of Merkel Cell Carcinoma Tumors

Project description:Array-CGH profiles of Merkel cell carcinoma tumors Keywords: fresh frozen and formalin fixed paraffin embedded primary tumor, nodal and metastasis merkel cell carcinoma tumor samples

2009-01-01 | GSE13239 | GEO

microRNA expression patterns related to merkel cell polyomavirus infection and clinical outcomes in human merkel cell carcinoma

Project description:We performed miRNA expression profiling in a series of human Merkel Cell carcinoma samples using a microarray approach. Significant differentially expressed miRNAs among groups were identified using SAM analysis. Agilent microarray platform containing 723 human miRNAs was used to determine miRNA expression profiles in 16 human Merkel cell carcinoma (MCC) samples. To validate the microarray platform, the expression levels of selected miRNAs were evaluated using qRT-PCR.

2013-12-31 | E-GEOD-43699 | biostudies-arrayexpress

Identification of an Enhancer RNA for EGFR in Hyper-accessible Regions in Esophageal Squamous Cell Carcinoma Cells by Analysis of Chromatin Accessibility Landscapes

Project description:To reveal the modified gene regulatory elements including transcription factors and enhancers in esophageal squamous carcinoma cells (ESCC), we performed Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) with two ESCC cell lines, i.e. KYSE-30 and KYSE-150, and a non-cancerous esophageal epithelial cell line, HET-1A. This data showed that hyper-accessible regions in ESCC cells contained genes related with cancer hallmarks including DNA replication and angiogenesis. Further motif analysis suggested that AP-1 family transcription factors bind the hyper-accessible regions in KYSE-30 cells as compared to those in HET-1A cells.

2021-11-04 | GSE162380 | GEO

Comparative genomic hybridization of human Merkel cell carcinoma tumors

Project description:Array-CGH profiles of Merkel cell carcinoma tumors Experiment Overall Design: We perfromed array-CGH on 25 Merkel cell carcinoma tumor samples (2 primary/metastasis pairs) looking for recurrent gains/losses among the cohort of tumors. Experiment Overall Design: Results from the Analysis of Copy Errors (ACE) may be found in GSE13239_MccACEAnalyzedData.txt. Experiment Overall Design: The overall profiles of the primary/metastasis pairs are similar. These metastases samples, 1m and 3m, were excluded from the ACE analysis.

2009-01-14 | E-GEOD-13239 | biostudies-arrayexpress

Identification of accessible chromatin regions in response to cold stress in Vitis amurensis

Project description:We report the Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) for high-throughput profiling of accessible chromatin regions after cold treatment in Vitis amurensis

2021-11-12 | GSE122487 | GEO

Proteome analysis of Merkel cell carcinoma cell lines using SILAC

Project description:Merkel cell carcinoma (MCC) is a rare and aggressive neuroendocrine tumor of the skin with growing incidence. In research immortalized cell lines are used for in vitro experiments in order to better understand the biology of this malignant disease.

2020-01-09 | PXD008181 | Pride

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