Single cell RNA-seq analysis on human endometrium across the natural menstrual cycle
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE111976 | GEO | 2020/06/29
REPOSITORIES: GEO
Similar Datasets
Project description:Background: Endometrial organoids are useful tools for studying endometrial biology but are derived from endoemtrial tissue obtained invasively from biopsies and mostly from women not taking hormonal medication. To increase the proportion of women from which endometrial organoids can be obtained, we sought to compare endometrial organoids derived from menstrual fluid and hormone-treated endometrium with standard endometrial organoids. Purpose: To determine if organoids derived from menstrual fluid and hormone-treated endometrium share features with standard endometrial organoids. Methods: RNA sequencing was performed on passage 3 day 7 menstrual fluid organoids (MFO), endometrial organoids from women taking hormonal medication (EMO-H) and standard endometrial organoids (EMO) Results: to determine if organoids derived from menstrual fluid and hormone-treated endometrium share features with staandard endometrial organoids. Conclusions: MFO and EMO-H did not cluster distinctly to EMO, indicating that they share features with EMO and may enable population-wide disease modelling. This is the first publicly available data set demonstrating the transcriptome of EMO-H.
2021-12-06 | GSE188915 | GEO
Project description:Background: a fundamental challenge for reproductive biology is to understand the menstrual cycle, specially the window of implantation, whose regulation and mechanistic remain incompletely understood in human reproductive physiology. Transcriptomics from a systems biology perspective provides a genomic framework to discover endometrial tissue specific regulation and behavior and its function in reproductive physiology. Results: Here, we applied a transcriptomic analysis of 238 endometrial receptivity related genes using a customized Agilent platform. 507 human endometrial biopsies were analyzed among the menstrual cycle, especially in the expected window of implantation and divided in to transcriptomic profiles using machine learning predictors (SVM and KNN models). The clinical relevance of these profiles was tested defining the best transcriptomic profile for pregnancy and live birth. Weighed Gene Co-expression Networks (WGCN) was applied is these clinically well-defined endometrial states to characterize the gene co-expression tissue specific regulation in humans for pregnancy in comparison with the other transcriptomic stages of menstrual cycle. For the first time, the menstrual cycle has been mapped as a percentage of positive and negative correlations between genes. Thanks to this approach, we have discovered the WOI as the fewest negatively correlated state with the highest proportion of positive correlations (Cochran´s Q = 14324.12, FDR < 2.2e-16) with an average of 84% of positive correlations in pregnant profile, while 53% in the two previous Proliferative (PF) and Early Pre-Receptive profiles and 67% in the late secretory endometrium, just before menstruation renewal. Finally, this study provides a wealth of network data to the scientific community to stimulate hypothesis-driven single-molecule endometrial studies in the form of a user-friendly database called the Menstrual Cycle Gene Co-expression Network (website: www.menstrualcyclegcn.com). Conclusions: this genomic research reveals for first time the pregnant endometrium as a global derepressed state in human menstrual cycle. This indicates the endometrium is generally a repressive tissue in human menstrual cycle with a relaxed WOI period where gene expression reaches the highest proportion of positive correlation, indicating that a decrease of inhibition may allow embryo implantation. Detailed molecular information about co-expression among menstrual cycle is also provided.
2021-09-15 | GSE126581 | GEO
Project description:Natural variability in menstrual cycle length, coupled with rapid changes in endometrial gene expression, makes it difficult to accurately define and compare different stages of the endometrial cycle. We have developed and validated a novel method for precisely determining endometrial cycle stage based on global gene expression. Our ‘molecular staging model’ reveals significant and remarkably synchronized daily changes in expression for over 3,400 endometrial genes throughout the cycle, with the most dramatic changes occurring during the secretory phase.
2023-09-06 | GSE234368 | GEO
Project description:To examine the possibility that biochemical or molecular signatures of endometrium may prove to be more useful, we have investigated whole genome molecular phenotyping (54,600 genes/ESTs) of this tissue sampled across the cycle in 28 normo-ovulatory women, using high-density oligonucleotide microarrays. The results demonstrate that endometrial samples obtained by two different sampling techniques (biopsy and curetting hysterectomy specimens) from subjects who are as normal as possible in a human study and 4 including those with unknown histology, can be classified by their molecular signatures and correspond to known phases of the menstrual cycle with identical results using two independent analytical methods. Also, the results enable global identification of biological processes and molecular mechanisms that occur dynamically in the endometrium in the changing steroid hormone milieu across the menstrual cycle in normo-ovulatory women. The results underscore the potential of gene expression profiling for developing molecular diagnostics of endometrial normalcy and abnormalities and identifying molecular targets for therapeutic purposes in endometrial disorders. Keywords: Gene expression arrays human endometrium
2006-05-24 | GSE4888 | GEO
Project description:The transition of regularly cycling endometrium from the proliferative or Estrogen-dominant phase of the menstrual cycle to the Progesterone-dominant Early and Mid Secretory phases requires wide-spread changes in gene expression that shift the endometrium from a proliferative capacity to a differentiated 'decidual' phenotype in preparation for implantation. This process appears delayed in women with severe endometriosis, suggestive of a progesterone resistant endometrium in this disease. Experiment Overall Design: Endometrial biopsies were obtained from women both with normal endometrial pathologies and no history of endometriosis and from women with laporoscopy proven moderate-severe stage endometriosis. Samples were collected from the Proliferative(PE), Early Secretory (ESE) and Midsecretory (MSE) phases. Samples were then processed for Total RNA isolation and Affymetrix chip hybridization.
2008-04-09 | E-GEOD-6364 | biostudies-arrayexpress
Project description:To examine the possibility that biochemical,or molecular signatures of endometrium may prove to be more useful, we have investigated,whole genome molecular phenotyping (54,600 genes/ESTs) of this tissue sampled across the,cycle in 28 normo-ovulatory women, using high-density oligonucleotide microarrays. The results demonstrate,that endometrial samples obtained by two different sampling techniques (biopsy and curetting,hysterectomy specimens) from subjects who are as normal as possible in a human study and,4,including those with unknown histology, can be classified by their molecular signatures and,correspond to known phases of the menstrual cycle with identical results using two independent,analytical methods. Also, the results enable global identification of biological processes and,molecular mechanisms that occur dynamically in the endometrium in the changing steroid,hormone milieu across the menstrual cycle in normo-ovulatory women. The results underscore,the potential of gene expression profiling for developing molecular diagnostics of endometrial,normalcy and abnormalities and identifying molecular targets for therapeutic purposes in,endometrial disorders.
2007-06-25 | E-GEOD-4888 | biostudies-arrayexpress
Project description:The aim of the experiment was to investigate the effects of stimulation of human endometrial organoids with estrogen (E2) and progesterone (P4) In humans, the endometrium, the uterine mucosal lining, undergoes dynamic changes throughout the menstrual cycle and in pregnancy. We adapted conditions used to establish human adult stem cell-derived organoid cultures to generate 3D cultures of human endometrium. Unlike other mucosal epithelia, the endometrium responds dramatically to ovarian sex hormones, estrogen (E2) and progesterone (P4), which regulate cyclical proliferation and differentiation of endometrial glands with concomitant dynamic temporal and spatial expression of their receptors, ERalpha and PR.
2017-04-11 | GSE94723 | GEO
Project description:Successful embryo implantation into a receptive endometrium requires mutual endometrial-embryo communication. Recently, the function of extracellular vehicles (EVs) in cell-to-cell interaction in embryo-maternal interactions has been investigated. We explored isolated endometrial derived EVs, using RL95-2 cells as a model of a receptive endometrium, influenced by menstrual cycle hormones estrogen (E2; proliferative phase) progesterone (P4; secretory phase) and estrogen plus progesterone (E2P4; the receptive phase). EV sized particles were isolated by differential centrifugation and size exclusion chromatography. Nanoparticle tracking analysis was used to examine the different concentration and size of particles and EV proteomic analysis per-formed using shotgun label-free mass spectrometry. Our results showed that although endome-trial derived EVs were secreted in numbers independent of hormonal stimulation, EVs sizes were statistically modified by it. Proteomics analysis showed that hormone treatment changes affect the endometrial EVs proteome, with proteins enhanced within the EV E2P4 group shown to be in-volved in different processes such as embryo implantation, endometrial receptivity, and embryo development, supporting the concept of a communication system between the embryo and the maternal endometrium via EVs.
2023-02-13 | PXD039764 | Pride
Project description:Repair after damage is essential for tissue homeostasis. Post-menstrual repair of the uterine endometrium is a unique cyclical manifestation of rapid, scar-free, tissue repair taking ~3-5 days. Skin repair post-wounding is slower (~2 weeks) and, in the case of chronic wounds, takes months/years to restore integrity. Herein, the unique ‘rapid-repair’ endometrial environment is translated to the ‘slower-repair’ skin environment. Menstrual fluid (MF), the milieu of post-menstrual endometrial repair, facilitates healing of endometrial and keratinocyte ‘wounds’ in vitro, promoting cellular adhesion and migration, stimulates keratinocyte migration in an ex vivo human skin-reconstruct model and promotes re-epithelialization in an in vivo porcine wound model. Proteomic analysis of MF identified a large number of proteins; several proteins were selected for further investigation, with the endometrium demonstrated as the source of these factors. Functionally, they promote repair of endometrial and keratinocyte wounds by promoting migration, differing significantly from currently available wound-repair treatments, which mainly promote proliferation. Development of these and other menstrual fluid factors into a ‘migration-inducing’ treatment paradigm will provide novel therapies for tissue repair.
2018-07-30 | PXD007234 | Pride
Project description:The inner uterine lining (endometrium) has been shown to have a distinct methylation pattern that changes throughout the menstrual cycle. However, not much is known about how the endometrial methylome affects endometrial receptivity to implanting embryo in the second half of the menstrual cycle. The aim of the present study was to use genome-wide technologies and a paired study design to characterize the endometrial methylome in pre-receptive and receptive endometrium sampled from 17 healthy women within the same menstrual cycle.
2017-06-20 | GSE90060 | GEO