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Genetically defined syngeneic mouse models of ovarian cancer as tools for the discovery of combination immunotherapy (WGS)

ABSTRACT: Purpose: There are three goals of this study of these analysis: 1. To compare the genomic, exome and chromatin accessiblity profiles of the specific engineered fallopian tube cells of high-grade serous tubo-ovarian cancer (HGSC) models (this study) using whole-exome-, whole-genome- and ATAC sequencing. Methods: Genomic DNA was extracted from the cell lines mentioned below. Conclusions: We conclude that whole-exome, whole-genome and ATAC-seq characterization would expedite genetic network analyses and permit the dissection of complex biological functions.

ORGANISM(S): Mus musculus

PROVIDER: GSE159254 | GEO | 2020/11/17

REPOSITORIES: GEO

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Genetically defined syngeneic mouse models of ovarian cancer as tools for the discovery of combination immunotherapy (Exome)

Project description:Purpose: There are three goals of this study: 1. To compare the genomic, exome and chromatin accessiblity profiles of the specific engineered fallopian tube cells of high-grade serous tubo-ovarian cancer (HGSC) models (this study) using whole-exome, whole-genome and ATAC-seq sequencing. Methods: For whole-exome analysis, genomic DNA was extracted from the cell lines mentioned below. Conclusions: We conclude that whole-exome, whole-genome and ATAC-seq characterization would expedite genetic network analyses and permit the dissection of complex biological functions.

2020-11-17 | GSE159253 | GEO

Genetically defined syngeneic mouse models of ovarian cancer as tools for the discovery of combination immunotherapy [scRNA-Seq]

Project description:Purpose: One of the goals of this study is to compare the transcriptome profiles of tumors from mice inoculated with specific engineered fallopian tube cells of high-grade serous tubo-ovarian cancer (HGSC) models (this study) using scRNA sequencing Methods: Tumors from mice inoculated with specific engineered fallopian tube cells of high-grade serous tubo-ovarian cancer (HGSC) models were compared using scRNA sequencing. Conclusions: We conclude that scRNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biological functions.

2020-11-17 | GSE158886 | GEO

Genetically defined syngeneic mouse models of ovarian cancer as tools for the discovery of combination immunotherapy (RNA-seq)

Project description:Purpose: One of the goals of this study is to compare the transcriptome profiles of tumors from mice inoculated with specific engineered fallopian tube cells of high-grade serous tubo-ovarian cancer (HGSC) models (this study) using next-generation sequencing (NGS)-derived RNA-seq. Methods: Tumors from mice inoculated with specific engineered fallopian tube cells of high-grade serous tubo-ovarian cancer (HGSC) models were compared using RNA sequencing. Conclusions: We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biological functions.

2020-11-17 | GSE158476 | GEO

ETV2 cooperates with SCL for timely gene activation during hemogenic endothelium specification [ATAC-Seq]

Project description:By performing ATAC sequencing in WT, Etv2KoiSCL and Etv2KOiETV2 ES cell derived day 4.75 endothelial cells, we report here ETV2 increases chromatin accessiblity at its binding sites.

2017-12-12 | GSE92534 | GEO

Epigenetic subtypes of neuroblastoma [ATAC-Seq]

Project description:In the absence of recurrent gene mutations, evidence accumulates that epigenetic deregulation plays a prominent role in neuroblastoma biology. Here we provide chromatin accessiblity profiles from ATAC-seq data in 2 neuroblastoma cell-lines.

2020-09-16 | GSE136279 | GEO

Relation between multi-gene mutation and in immune microenviroment in colorectal cancer

Project description:Interventions: NA:No Primary outcome(s): Whole exome;PFS Study Design: Cross-sectional

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Enhanced efficacy of aurora kinase inhibitors in G2/M checkpoint deficient TP53 mutant uterine carcinomas is linked to the summation of LKB1-AKT-p53 interactions [WGS]

Project description:We report bulk RNA sequencing, low pass whole genome sequencing, and targeted exome sequencing data of six uterine cancer organoids and show how specific molecular defects in these organoids make them sensitive to cell cycle targeting therapies.

2021-05-08 | GSE171515 | GEO

The proneural transcription factor ASCL1 regulates cell proliferation and primes for differentiation in neuroblastoma [ATAC-seq]

Project description:To compare the function of endogenous ASCL1 in different neuroblastoma cell contexts, we have used CRISPR-mediated deletion to compare the effects of ASCL1 deletion in a MYCN-amplified and an ALK-driven neuroblastoma line and assessed the impact of ASCL1 knockout on chromatin accessiblity genome-wide using ATAC-seq

2022-08-31 | GSE202629 | GEO

The molecular landscape of homologous recombination deficient, end-stage, high grade serous ovarian cancer

Project description:High grade serous cancer (HGSC) is frequently characterizsed by homologous recombination (HR) DNA repair deficiency, and while most such tumours are sensitive to initial treatment, acquired resistance is common. We undertook a multi-omics approach to interrogating mechanisms of resistance, using multiple autopsy samples collected from 15 women with HR-deficient HGSC. We observed frequent reversion mutations, resistance mechanisms restoring HR by other means, a high frequency of whole-genome duplication (WGD) suggestive of an evolutionary advantage, and global changes in immune composition with evidence of immune escape. Collectively these findings have implications for therapeutic intervention for HR-deficient HGSC.

2023-02-27 | PXD030034 | Pride

Expression data from high-grade serous ovarian carcinomas (HGSC), clear cell ovarian carcinomas (CCC) and ovarian surface epithelium (OSE)

Project description:Background: The aim of this study was to identify differentially expressed miRNAs in high-grade serous ovarian carcinoma (HGSC), clear cell ovarian carcinoma (CCC) and ovarian surface epithelium (OSE). Selected miRNAs were evaluated for association with clinical parameters including survival, and miRNA/mRNA interactions were mapped. Results: Differentially expressed miRNAs between HGSC, CCC and OSE were identified, of which 18 were validated (p<0.01) using RT-qPCR in an extended cohort. Compared with OSE, miR-205-5p was the most overexpressed miRNA in HGSC. miR-200 family members and miR-182-5p were the most overexpressed in HGSC and CCC compared with OSE, whereas miR-383 was the most underexpressed. miR-509-3-5p, miR-509-5p, miR-509-3p and miR-510 were among the strongest differentiators between HGSC and CCC, all being significantly overexpressed in CCC compared with HGSC. High miR-200c-3p expression was associated with poor progression-free (p=0.031) and overall (p=0.026) survival in HGSC. Interacting miRNAs and mRNA targets, including those of a TP53-related pathway presented previously, were identified in HGSC. Conclusions: Several miRNAs are overexpressed in HGSC and CCC compared with OSE, including the miR-200 family, among which miR-200c-3p is associated with survival in HGSC. A set of miRNAs differentiates CCC from HGSC, of which miR-509-3-5p and miR-509-5p are the strongest classifiers. Several interactions between miRNAs and mRNAs in HGSC were mapped. Methods: Differences in miRNA expression between HGSC, CCC and OSE scrapings were analyzed by global miRNA expression profiling (Affymetrix GeneChip miRNA 2.0 Arrays, n=30), validated by RT-qPCR (n=63), and evaluated for associations with clinical parameters. For HGSC, differentially expressed miRNAs were linked to differentially expressed mRNAs identified previously (GSE36668).

2014-02-13 | E-GEOD-47841 | biostudies-arrayexpress

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