Genome-wide histone modification profiling in endometriosis cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE86810 | GEO | 2017/04/05
SECONDARY ACCESSION(S): PRJNA342603
REPOSITORIES: GEO
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Project description:We show that knocking down ARID1A in an immortalized endometriosis cell line leads to phenotypic changes in vitro. Additionally, we find strong increases in the active H3K27ac mark in promoter regions but decrease of H3K27ac at potential enhancers with targeted DNA methylation-independent alterations in nucleosome occupancy.
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Project description:Down-regulation of ARID1A in endometriosis cells leads to gene expression alterations.
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Project description:We performed gene expression analysis human peritoneal endometriosis lesions, eutopic endometrium from endometriosis patients and peritoneum form endometriosis patients.The goal of the study was to analyse gene expression differences between peritoneal endometriosis lesion and eutopic endometrium and peritoneal endometriosis lesion and peritoneum.
2012-12-06 | E-MTAB-694 | biostudies-arrayexpress
Project description:We analyzed ChIP-seq profiles for H3K4me3, H3K27ac, BRG1, ARID1A, PPAR? and JMJD1A and FAIRE-seq open chromatin profile in immortalized brown adipocytes (iBATs) treated with 1 ?M isporoterenol (ISO) or vehicle for 2 hr ChIP-seq profiles for H3K4me3, H3K27ac, BRG1, ARID1A, PPAR? and JMJD1A and FAIRE-seq open chromatin profile in iBATs at Day 8 of differentiation treated with 1 ?M isporoterenol (ISO) or vehicle for 2 hr
2015-04-15 | E-GEOD-67586 | biostudies-arrayexpress
Project description:This project aims at comparing endometrium from women with and without endometriosis during the secretory phase of menstrual cycle. The present results constitute a first step towards identifying potential diagnosis biomarkers and may provide a better understanding of endometriosis especially the etiology of the disease.
2022-04-01 | PXD012981 | Pride
Project description:A discovery study using RNA-HighSeq from 37 endometrial biopsies was performed to build classifiers that differentiate between control patients and adenomyosis, ovarian endometriosis and deep infiltrating endometriosis. Total RNA was extracted from endometrial biopsies. We found an AUC of 0.97 where the classifier differentiated almost perfectly all three diseases together from the control group when including 11 phenotypic variables of the patients in the classifier.
2024-01-31 | GSE193928 | GEO
Project description:Mechanisms of immune dysregulation against established tumors are relatively well understood. Much less is known about the role of immune effectors against cancer precursor lesions. Endometrioid and clear cell ovarian tumors may partly derive from endometriosis, a commonly diagnosed chronic inflammatory disease. We performed here the most comprehensive immune gene expression analysis of pelvic inflammation in endometriosis and endometriosis-associated ovarian cancer (EAOC). RNA was extracted from 120 paraffin tissue blocks comprising of normal endometrium (n=32), benign endometriosis (n=30), atypical endometriosis (n=15) and EAOC (n=43). Serous tumors (n=15) were included as non-endometriosis associated controls. The immune microenvironment was profiled using Nanostring and the nCounter® GX Human Immunology Kit, comprising probes for a total of 511 immune genes. Please note that 3 normal endometrium samples did not pass the array quality filtering and therefore excluded in the data analyses.
2015-01-07 | E-GEOD-57545 | biostudies-arrayexpress
Project description:Purpose: This study was undertaken to evaluate the effect of peritoneal fluid from subjects with differing stages of endometriosis on gene expression in endometrial stromal cells. Methods: Peritoneal fluid from subjects with minimal, moderate, and severe stages of endometriosis or without endometriosis (controls) was collected, filtered and separated from peritoneal cells. Telomerase – immortalized human endometrial stromal cells (T-HESC) were treated with the peritoneal fluid samples for 48 hours. RNA was isolated from treated cells and processed for DNA microarray. Results: 162 genes were found to be differentially expressed in T-HESC cells treated with peritoneal fluid from subjects with differing stages of endometriosis. Three of the differentially expressed genes were chosen for confirmatory studies using quantitative RT-PCR; these were interleukin 8, corin and matrix metalloproteinase 3. The primary gene ontologies identified by microarray highlight functions expected to be involved in the establishment of endometriosis, such as proteases, signal transduction, defense and immune system, cell adhesion, cell cycle and cell death, cytoskeleton, transcriptional regulation and translation, extracellular matrix, and enzymes and metabolism. Conclusions: This study demonstrated that the severity of endometriosis affected the factors present in peritoneal fluid which, in turn, affected gene expression in endometrial stromal cells.
2019-07-01 | GSE101176 | GEO
Project description:Endometriosis is a debilitating gynecological disorder affecting approximately 10% of the female population. Despite its prevalence, robust methods to classify and treat endometriosis remain elusive. Changes throughout the menstrual cycle in tissue size, architecture, cellular composition, and individual cell phenotypes make it extraordinarily challenging to identify markers or cell types associated with uterine pathologies since disease-state alterations in gene and protein expression are convoluted with cycle phase variations. Here, we developed an integrated workflow to generate both proteomic and single-cell RNA-sequencing (scRNA-seq) data sets using tissues and cells isolated from the uteri of control and endometriotic donors. Using a linear mixed effect model (LMM), we identified proteins associated with cycle stage and disease, revealing a set of genes that drive separation across these two biological variables. Further, we analyzed our scRNA-seq data to identify cell types expressing cycle and disease- associated genes identified in our proteomic data. A module scoring approach was used to identify cell types driving the enrichment of certain biological pathways, revealing several pathways of interest across different cell subpopulations. Finally, we identified ligand-receptor pairs including Axl/Tyro3 – Gas6, that may modulate interactions between endometrial macrophages and/or endometrial stromal/epithelial cells. Analysis of these signaling pathways in an independent cohort of endometrial biopsies revealed a significant decrease in Tyro3 expression in patients with endometriosis compared to controls, both transcriptionally and through histological staining. This measured decrease in Tryo3 in patients with disease could serve as a novel diagnostic biomarker or treatment avenue for patients with endometriosis. Taken together, this integrated approach provides a framework for integrating LMMs, proteomic and RNA-seq data to deconvolve the complexities of complex uterine diseases and identify novel genes and pathways underlying endometriosis.
2023-09-05 | PXD045115 | Pride
Project description:Endometriosis is a complex pathological condition in which multiple components are involved in the disease development and clinical outcome. Endometriosis is mainly an inflammatory codition estrogen-dependent, with unknown pathogenesis, that is characterized by dissemination of edometrium tissue in ectopic position (ovary or pelvic peritoneum). Two main theories rise the pathologic onset: the presence of retrograde menstruation and celomic metaplasia in the pelvic peritoneum, that can occur for development defects. Endometriosis is related not only to genetic or immunological changes and to environmental pollution factors, as the endocrine interferents. The disease phenotype results from multiple events (genetics and enviromental), thus it is difficult to find a single gene as causative while is more probable that a gene network/s might involved in the onset and mantainement of the disease state. The peculiarity of endometriosis rely on the tissue speificity manteinance in the ectopic position, where it responds to the hormone stimuli as the tissue in the eutopic position. In order to identify genes potentially involved in growth and mainteinance of the ectopic endometrium, we have profiled ectopic (8 samples) and eutopic endometrium (8 samples) from several affected woman in the proliferative phase. As control we used endometrium from normal health donors in the same phase (6 samples).
2013-11-30 | E-GEOD-25628 | biostudies-arrayexpress