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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Examining the effect of SMARCA4–p53 regulatory axis on SCCOHT cells transcription

ABSTRACT: To examine the role SMARCA4-p53 regulatory axis in SCCOHT cells we performed RNA-seq in BIN-67 cells with SMARCA4 restoration, p53ko alone or combined with SMARCA4 and idasanutlin treatment (0.5μM, 24h) which increase the stability of p53 and its protein levels in SCCOHT.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Giulio Aceto

PROVIDER: E-MTAB-15707 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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To examine the role of p300 in the SMARCA4–p53 regulatory axis, we performed ChIP-seq to assess p300, p53, H3K27ac, HDAC1, HDAC2 occupancy in BIN-67 cells

Project description:ChIP-seq was performed in BIN-67, BIN-67 p53ko, BIN-67 with SMARCA4 restoration and BIN-67 p53ko cells with SMARCA4 restoration to assess the impact of SMARCA4 and p53 on the pull downs of p300, H3K27ac, p53, HDAC1 and HDAC2.

2026-05-05 | E-MTAB-15700 | biostudies-arrayexpress

Assessing SMARCA4 restoration contribution to global changes in p300 occupancy in BIN-67 cells

Project description:We aim to test how SMARCA4 restoration impacts p300 occupancy distribution. To this aim we generated ChIP-seq samples in BIN-67 with or without A-485 treatment (1 μM, 24h), as a proxy for p300 acetylatransferase inhibition, and BIN-67 with inducible SMARCA4 restoration (1 μg/ml Doxycycline for 24h). We pulled down p300 and H3K27ac as a marker for p300 acetyltransferase activity on the chromatin.

2026-05-05 | E-MTAB-15699 | biostudies-arrayexpress

p53-ko rescues gene expression changes mediated by p300 acetyltransferase inhibition

Project description:RNA-seq samples in BIN-67 and BIN-67p53-ko cells with or without A-485 treatment (1μM, 24h). The goal of the experiment is to assess the genes that are regulated by p300 acetyltransferase inhibition using A-485 treatment and weather p53-ko can rescue this phenotype.

2026-05-05 | E-MTAB-15706 | biostudies-arrayexpress

Long term and short term Idasanutlin treatments in SCCOHT cell lines

Project description:RNA-seq samples in SCCOHT-1 and COV434 for idasanutlin treatment (0.5μM, 24h), and RNA-seq samples in BIN-67 and COV434 for short-term idasanutlin treatment (0.5μM, 3h). The goal of the experiment is to assess the genes that are regulated by p53 stabilization in the long term or short term using idasanutlin treatment in SCCOHT.

2026-05-05 | E-MTAB-16956 | biostudies-arrayexpress

EP300 acetyltransferase inhibition in SCCOHT cell lines

Project description:RNA-seq samples in BIN-67, COV434, SCCOHT-1 cells including Control (Ctrl.) and A-485 treatment (24h, 1μM)

2026-05-05 | E-MTAB-15705 | biostudies-arrayexpress

Re-expression of SMARCA4/BRG1 in Small Cell Carcinoma of Ovary, Hypercalcemic Type (SCCOHT) promotes an epithelial-like gene signature through an AP-1-dependent mechanism

Project description:Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is a rare and aggressive form of ovarian cancer. SCCOHT tumors have inactivating mutations in SMARCA4 (BRG1), one of the two mutually exclusive ATPases of the SWI/SNF chromatin remodeling complex. To address the role that BRG1 loss plays in SCCOHT tumorigenesis, we performed integrative multi-omic analyses in SCCOHT cell lines +/- BRG1 re-expression. BRG1 re-expression induced a gene and protein signature similar to an epithelial cell and gained chromatin accessibility sites correlated with other epithelial originating TCGA tumors. Furthermore, AP-1 motifs were enriched at the promoters of highly upregulated epithelial genes. Using a dominant negative AP-1 cell line, we found that both AP-1 DNA binding activity and BRG1 re-expression are necessary for the gene and protein expression of epithelial genes. Our study demonstrates that BRG1 re-expression drives an epithelial-like gene and protein signature in SCCOHT cells that depends upon AP-1 activity.

2021-01-15 | PXD014134 | Pride

BIN-67 small cell ovarian carcinoma SNP array

Project description:The biology of small cell ovarian carcinoma of the hypercalcemic type (SCCOHT), which is a rare and aggressive form of ovarian cancer, is poorly understood. Tumourigenicity, in vitro growth characteristics, genetic and genomic anomalies, and sensitivity to standard and novel chemotherapeutic treatments were investigated in the unique SCCOHT cell line, BIN-67, to provide further insight in the biology of this rare type of ovarian cancer. Chromosomal anomalies in BIN-67 cells were inferred using the Infinium? genotyping technology with the HumanHap300-Duo Genotyping BeadChip (Illumina, San Diego, CA, USA). This BeadChip contains about 318,000 genetic markers within approximately a 5 kb median SNP spacing. Genotyping and imaging using BeadStudio Data Analysis software (Illumina, San Diego, CA, USA) were performed at the McGill University and Genome Quebec Innovation Centre (Montreal, QC).

2013-09-24 | E-MTAB-1584 | biostudies-arrayexpress

BIN-67 small cell ovarian carcinoma Expression array

Project description:The biology of small cell ovarian carcinoma of the hypercalcemic type (SCCOHT), which is a rare and aggressive form of ovarian cancer, is poorly understood. Tumourigenicity, in vitro growth characteristics, genetic and genomic anomalies, and sensitivity to standard and novel chemotherapeutic treatments were investigated in the unique SCCOHT cell line, BIN-67, to provide further insight in the biology of this rare type of ovarian cancer. Microarray expression analysis was performed using the GeneChip? Human Genome U133 Plus 2.0 Array (Affymetrix?, Santa Clara, CA) with total RNA from BIN-67 cells. Hybridization and scanning were performed at the McGill University and Genome Quebec Innovation Centre (Montreal, QC). Gene expression levels were determined from the scanned images using Affymetrix? Microarray Suite (MAS) version 5.0 software expression algorithm (Affymetrix?, Santa Clara, CA). Gene expression profiles were compared with Affymetrix U133 Plus 2.0 (MAS5.0) generated expression profiles (similarly normalized) from 10 human normal ovarian surface epithelial (OSE) cell brushings available in the ArrayExpress database (www.ebi.ac.uk/arrayexpress/), accession number E-GEOD-18520.

2013-09-24 | E-MEXP-3872 | biostudies-arrayexpress

Gene expression in small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) cell line COV434

2025-04-02 | GSE217699 | GEO

SMARCA4-loss increases RNA Polymerase II pausing and elevates R-loops to inhibit BRCA1-mediated repair in ovarian cancer

Project description:Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is a rare and aggressive cancer mainly affecting young women. It is driven by inactivating mutations in SMARCA4 (BRG1), a key SWI/SNF chromatin remodeling gene. To reveal its druggable vulnerabilities, we perform a compound screen and find that SCCOHT cells and tumors are sensitive to PARP inhibitors. Paradoxically, SCCOHT displays BRCA-deficient traits while retaining wild-type BRCA1 expression. This is caused by elevated R-loop accumulation in SCCOHT cells and tumors, which sequesters BRCA1 limiting its availability for DNA damage repair. Through proximity-dependent biotin identification approach using pathogenic SMARCA4 variants that retain protein expression, we uncover that SMARCA4 promotes RNA polymerase II (Pol II) elongation by mediating the assembly of the polymerase-associated factor 1 (PAF1) complex and its association with Pol II. Thus, SMARCA4 loss increases Pol II pausing, resulting in elevated R-loops and BRCA1 redistribution. This leads to the sensitivity of SCCOHT cells and tumors to PARP inhibitors, which is further enhanced by addition of a CDK9 inhibitor targeting Pol II elongation. Our findings reveal a link between SMARCA4 loss and perturbed Pol II elongation causing hampered BRCA1 repair, which can be exploited therapeutically to target SCCOHT. (These studies were supported by Canadian Institute of Health Research (CIHR) grants PJT-156233 and PJT-438303).

2025-04-24 | GSE290811 | GEO

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