scholarly journals Coupling miR/isomiR and mRNA Expression Signatures Unveils New Molecular Layers of Endometrial Receptivity

Life ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1391
Author(s):  
Maria Nikolova ◽  
Mladen Naydenov ◽  
Ilias Glogovitis ◽  
Apostol Apostolov ◽  
Merli Saare ◽  
...  
Keyword(s):  
Rapid Development ◽  
Expression Patterns ◽  
Embryo Implantation ◽  
Endometrial Receptivity ◽  
Joint Analysis ◽  
Gene Target ◽  
Mrna Targets ◽  
Sequencing Technologies ◽  
Significant Expression ◽  
Molecular Layers

Embryo implantation depends on endometrial receptivity (ER). To achieve ER, the preparation of the uterine lining requires controlled priming by ovarian hormones and the expression of numerous genes in the endometrial tissue. microRNAs (miRs) have emerged as critical genetic regulators of ER in fertility and of the diseases that are associated with infertility. With the rapid development of next-generation sequencing technologies, it has become clear that miR genes can produce canonical miRs and variants—isomiRs. Here, we describe miR/isomiR expression dynamics across the four time points of natural chorionic gonadotropin (hCG)-administered cycles. Sequencing of the small RNAs (sRNA-seq) revealed that the most significant expression changes during the transition from the pre-receptive to the receptive phase occurred in the isomiR families of miR-125a, miR-125b, miR-10a, miR-10b, miR-449c, miR-92a, miR-92b, and miR-99a. Pairing the analysis of the differentially expressed (DE) miRs/isomiRs and their predicted DE mRNA targets uncovered 280 negatively correlating pairs. In the receptive endometrium, the 5’3’-isomiRs of miR-449c, which were among the most highly up-regulated isomiRs, showed a negative correlation with their target, transcription factor (TF) MYCN, which was down-regulated. Joint analysis of the miR/isomiR and TF expression identified several regulatory interactions. Based on these data, a regulatory TF-miR/isomiR gene-target circuit including let7g-5p and miR-345; the isomiR families of miR-10a, miR-10b, miR-92a, and miR-449c; and MYCN and TWIST1 was proposed to play a key role in the establishment of ER. Our work uncovers the complexity and dynamics of the endometrial isomiRs that can act cooperatively with miRs to control the functionally important genes that are critical to ER. Further studies of miR/isomiR expression patterns that are paired with those of their target mRNAs may provide a more in-depth picture of the endometrial pathologies that are associated with implantation failure.

scholarly journals Endometrial Perivascular Progenitor Cells and Uterus Regeneration

2021 ◽  
Vol 11 (6) ◽  
pp. 477
Author(s):  
Shiyuan Li ◽  
Lijun Ding
Keyword(s):  
Stem Cells ◽  
Mesenchymal Stem Cells ◽  
Embryo Implantation ◽  
Endometrial Receptivity ◽  
Perivascular Cells ◽  
Asherman’S Syndrome ◽  
Outermost Layer ◽  
Adventitial Cells ◽  
Structure And Functions ◽  
Large Vessels

Ovarian steroid-regulated cyclical regeneration of the endometrium is crucial for endometrial receptivity and embryo implantation, and it is dependent on the dynamic remodeling of the endometrial vasculature. Perivascular cells, including pericytes surrounding capillaries and microvessels and adventitial cells located in the outermost layer of large vessels, show properties of mesenchymal stem cells, and they are thus promising candidates for uterine regeneration. In this review, we discuss the structure and functions of the endometrial blood vasculature and their roles in endometrial regeneration, the main biomarkers and characteristics of perivascular cells in the endometrium, and stem cell-based angiogenetic therapy for Asherman’s syndrome.

scholarly journals Bu Shen Zhu Yun Decoction Improves Endometrial Receptivity via VEGFR-2-Mediated Angiogenesis

2019 ◽  
Vol 2019 ◽  
pp. 1-14 ◽  
Author(s):  
Li Li ◽  
Huabo Jiang ◽  
Xuecong Wei ◽  
Dandan Geng ◽  
Ming He ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Embryo Implantation ◽  
Mapk Signaling ◽  
Endometrial Receptivity ◽  
Mapk Signaling Pathway ◽  
Mitogen Activated Protein Kinase ◽  
Cell Counting ◽  
Nuclear Antigen ◽  
Vitro Fertilization

Vascular endothelial growth factor receptor-2 (VEGFR-2) regulates the mitogen-activated protein kinase (MAPK) signaling pathway and plays an important role in angiogenesis. Bu Shen Zhu Yun decoction (BSZYD) can improve endometrial receptivity and embryo implantation rates in patients undergoing in vitro fertilization. However, whether BSZYD improves endometrial receptivity via angiogenesis remains unclear. Here, we investigated the effects of BSZYD on the proliferation, migration, and angiogenesis of human endometrial microvascular endothelial cells (HEMECs) and found that BSZYD upregulated the expression of cyclin D1, matrix metalloproteinase 9 (MMP9), and proliferating cell nuclear antigen (PCNA) in HEMECs. Cell Counting Kit 8 assay, scratch-wound assay, and Tube Formation Assay results showed that BSZYD promoted the proliferation, migration, and angiogenesis of HEMECs. Western blot analysis results revealed the activation of the MAPK signaling pathway by BSZYD through the upregulation of VEGF and VEGFR-2 expression. Together, these findings highlight the novel mechanism underlying BSZYD-mediated improvement in endometrial receptivity through the MAPK signaling pathway.

Abstract 837: Beta1 And Beta2 Adrenergic Receptor Transgenic Mice Display Distinct MicroRNA Expression Patterns That Converge On The Hypertrophic Signature

Circulation ◽  
2007 ◽  
Vol 116 (suppl_16) ◽  
Author(s):  
Danish Sayed ◽  
Shweta Rane ◽  
Leng-Yi Chen ◽  
Minzhen He ◽  
Jacqueline Lypowy ◽  
...  
Keyword(s):  
Cardiac Hypertrophy ◽  
Adrenergic Receptor ◽  
Mapk Pathway ◽  
Expression Patterns ◽  
Pressure Overload ◽  
Mapk Signaling ◽  
Compensatory Hypertrophy ◽  
Over Expression ◽  
Mrna Targets ◽  
Dose Dependent

MicroRNA (miRNA) are ~22 ribonucleotides-long, with a potential to recognize multiple mRNA targets guided by sequence complimentarity. This class of molecules is functionally versatile, with the capacity to specifically inhibit translation, as well as, induce mRNA degradation, through targeting the 3′-untranslated regions. The levels of individual miRNA vary under different developmental, biological, or pathological conditions, thus, implicating them in normal and pathological cellular attributes. We have previously reported a miRNA signature that distinguishes pressure-overload compensatory hypertrophy by recapitulating the neonatal pattern. We hypothesized that this ’signature’ might aid in discriminating the underlying molecular differences in genetic models of cardiac hypertrophy, as seen in the beta1 and 2 adrenergic receptor (B1AR and B2AR) transgenic (Tg) mice. To address this, we used microarray analysis of RNA isolated from the hearts of 3 months old B1AR and B2AR mice. In general, while both mice exhibited an overlap with the hypertrophy signature including, upregulation of miR-21 and downregulation of miR-133a, miR-133b, and miR-185, the B2-AR Tg exhibited a more extensive overlap with the hypertrophy pattern, which further included upregulation of miR-199a*, miR-214, and miR-15b. To understand the functional significance of these miRNA in myocyte hypertrophy, we cloned them and their anti-sense sequences into adenoviral vectors. Significantly, over-expression miR-21 resulted in a, dose-dependent, branching (sprouting) of the cells. Computational predictions by ’TargetScanS’ identified sprouty as potential target. Subsequently, we confirmed down-regulation of sprouty by over-expression of miR-21 and vice versa. Sprouty is a known inhibitor of the Ras-MAPK signaling pathway and is, concordantly, downregulated in many forms of cancer. In the heart, sprouty has been suggested to control myocyte size and vascularization during cardiac hypertrophy. Thus, we propose that B1AR and B2AR Tg models exhibit distinct miRNA profiles that converge on that of pressure-overload cardiac hypertrophy. Moreover, the commonly over-expressed miR-21 plays a role in downregulating sprouty, an antagonist of the Ras-MAPK pathway.

scholarly journals A Two-Cohort RNA-seq Study Reveals Changes in Endometrial and Blood miRNome in Fertile and Infertile Women

Genes ◽  
2018 ◽  
Vol 9 (12) ◽  
pp. 574 ◽  
Author(s):  
Kadri Rekker ◽  
Signe Altmäe ◽  
Marina Suhorutshenko ◽  
Maire Peters ◽  
Juan F. Martinez-Blanch ◽  
...  
Keyword(s):  
Embryo Implantation ◽  
Endometrial Receptivity ◽  
Small Rna Sequencing ◽  
Rna Seq ◽  
Recurrent Implantation Failure ◽  
Secretory Phase ◽  
Blood Samples ◽  
Infertile Women ◽  
Secretory Endometrium ◽  
Fertile Women

The endometrium undergoes extensive changes to prepare for embryo implantation and microRNAs (miRNAs) have been described as playing a significant role in the regulation of endometrial receptivity. However, there is no consensus about the miRNAs involved in mid-secretory endometrial functions. We analysed the complete endometrial miRNome from early secretory (pre-receptive) and mid-secretory (receptive) phases from fertile women and from patients with recurrent implantation failure (RIF) to reveal differentially expressed (DE) miRNAs in the mid-secretory endometrium. Furthermore, we investigated whether the overall changes during early to mid-secretory phase transition and with RIF condition could be reflected in blood miRNA profiles. In total, 116 endometrial and 114 matched blood samples collected from two different population cohorts were subjected to small RNA sequencing. Among fertile women, 91 DE miRNAs were identified in the mid-secretory vs. early secretory endometrium, while no differences were found in the corresponding blood samples. The comparison of mid-secretory phase samples between fertile and infertile women revealed 21 DE miRNAs from the endometrium and one from blood samples. Among discovered novel miRNAs, chr2_4401 was validated and showed up-regulation in the mid-secretory endometrium. Besides novel findings, we confirmed the involvement of miR-30 and miR-200 family members in mid-secretory endometrial functions.

scholarly journals LeafGo: Leaf to Genome, a quick workflow to produce high-quality De novo genomes with Third Generation Sequencing technology

2021 ◽  
Author(s):  
Patrick Driguez ◽  
Salim Bougouffa ◽  
Karen Carty ◽  
Alexander Putra ◽  
Kamel Jabbari ◽  
...  
Keyword(s):  
De Novo ◽  
Rapid Development ◽  
Plant Genome ◽  
Plant Genomics ◽  
High Quality ◽  
High Molecular Weight Dna ◽  
Tissue Samples ◽  
Sequencing Technologies ◽  
The Cost ◽  
New Generation

AbstractRecent years have witnessed a rapid development of sequencing technologies. Fundamental differences and limitations among various platforms impact the time, the cost and the accuracy for sequencing whole genomes. Here we designed a complete de novo plant genome generation workflow that starts from plant tissue samples and produces high-quality draft genomes with relatively modest laboratory and bioinformatic resources within seven days. To optimize our workflow we selected different species of plants which were used to extract high molecular weight DNA, to make PacBio and ONT libraries for sequencing with the Sequel I, Sequel II and GridION platforms. We assembled high-quality draft genomes of two different Eucalyptus species E. rudis, and E. camaldulensis to chromosome level without using additional scaffolding technologies. For the rapid production of de novo genome assembly of plant species we showed that our DNA extraction protocol followed by PacBio high fidelity sequencing, and assembly with new generation assemblers such as hifiasm produce excellent results. Our findings will be a valuable benchmark for groups planning wet- and dry-lab plant genomics research and for high throughput plant genomics initiatives.

scholarly journals SOMDE: A scalable method for identifying spatially variable genes with self-organizing map

2020 ◽  
Author(s):  
Minsheng Hao ◽  
Kui Hua ◽  
Xuegong Zhang
Keyword(s):  
Gene Expression ◽  
Large Scale ◽  
Expression Patterns ◽  
Self Organizing Map ◽  
Expression Data ◽  
Spatial Expression ◽  
Variable Expression ◽  
Sequencing Technologies ◽  
Physical Context ◽  
Variable Genes

AbstractRecent developments of spatial transcriptomic sequencing technologies provide powerful tools for understanding cells in the physical context of tissue micro-environments. A fundamental task in spatial gene expression analysis is to identify genes with spatially variable expression patterns, or spatially variable genes (SVgenes). Several computational methods have been developed for this task. Their high computational complexity limited their scalability to the latest and future large-scale spatial expression data.We present SOMDE, an efficient method for identifying SVgenes in large-scale spatial expression data. SOMDE uses selforganizing map (SOM) to cluster neighboring cells into nodes, and then uses a Gaussian Process to fit the node-level spatial gene expression to identify SVgenes. Experiments show that SOMDE is about 5-50 times faster than existing methods with comparable results. The adjustable resolution of SOMDE makes it the only method that can give results in ~5 minutes in large datasets of more than 20,000 sequencing sites. SOMDE is available as a python package on PyPI at https://pypi.org/project/somde.

scholarly journals Projecting genetic associations through gene expression patterns highlights disease etiology and drug mechanisms

2021 ◽  
Author(s):  
Milton Pividori ◽  
Sumei Lu ◽  
Binglan Li ◽  
Chun Su ◽  
Matthew E. Johnson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Association Studies ◽  
Expression Patterns ◽  
Cell Types ◽  
Joint Analysis ◽  
Genetic Associations ◽  
Disease Etiology ◽  
Mediating Role ◽  
Gene Modules ◽  
Trait Associations

Understanding how dysregulated transcriptional processes result in tissue-specific pathology requires a mechanistic interpretation of expression regulation across different cell types. It has been shown that this insight is key for the development of new therapies. These mechanisms can be identified with transcriptome-wide association studies (TWAS), which have represented an important step forward to test the mediating role of gene expression in GWAS associations. However, due to pervasive eQTL sharing across tissues, TWAS has not been successful in identifying causal tissues, and other methods generally do not take advantage of the large amounts of RNA-seq data publicly available. Here we introduce a polygenic approach that leverages gene modules (genes with similar co-expression patterns) to project both gene-trait associations and pharmacological perturbation data into a common latent representation for a joint analysis. We observed that diseases were significantly associated with gene modules expressed in relevant cell types, such as hypothyroidism with T cells and thyroid, hypertension and lipids with adipose tissue, and coronary artery disease with cardiomyocytes. Our approach was more accurate in predicting known drug-disease pairs and revealed stable trait clusters, including a complex branch involving lipids with cardiovascular, autoimmune, and neuropsychiatric disorders. Furthermore, using a CRISPR-screen, we show that genes involved in lipid regulation exhibit more consistent trait associations through gene modules than individual genes. Our results suggest that a gene module perspective can contextualize genetic associations and prioritize alternative treatment targets when GWAS hits are not druggable.

scholarly journals Plasticity of gene expression according to salinity in the testis of broodstock and F1 black-chinned tilapia, Sarotherodon melanotheron heudelotii

2014 ◽  
Author(s):  
Jean-Christophe Avarre ◽  
Bruno Guinand ◽  
Rémi Dugué ◽  
Jacky Cosson ◽  
Marc Legendre ◽  
...  
Keyword(s):  
Gene Expression ◽  
Natural Habitat ◽  
Expression Patterns ◽  
Osmotic Tolerance ◽  
Two Generations ◽  
Hypersaline Water ◽  
Significant Expression ◽  
Physiological Impact ◽  
High Level ◽  
Sarotherodon Melanotheron

The black-chinned tilapia Sarotherodon melanotheron heudelotii Rüppell 1852 (Teleostei, Cichlidae) displays remarkable acclimation capacities. When exposed to drastic changes of salinity, which can be the case in its natural habitat, it develops quick physiological responses and keeps reproducing. The present study focused on the physiological impact of salinity on male reproductive capacities, using gene expression as a proxy of acclimation process. Two series of experimental fish were investigated: the first one was composed of fish maintained in freshwater for several generations and newly acclimated to salinities of 35 and 70, whereas the second one consisted of the descendants of the latter born and raised under their native salinity. Expression patterns of 43 candidate genes previously identified from the testes of wild males was investigated in the three salinities and two generations. Twenty of them showed significant expression differences between salinities, and their predicted function revealed that most of them are involved in the osmotic tolerance of sperm cells and/or in the maintenance of sperm motility. A high level of expression variation was evidenced, especially for fish maintained in freshwater. In spite of this, gene expression patterns allowed the differentiation between fish raised in freshwater and those maintained in hypersaline water, in both generations. Altogether, the results presented here suggest that this high variability of expression is likely to ensure the reproductive success of this species under varying salinities.

Endometrial Receptivity and Human Embryo Implantation

2011 ◽  
Vol 66 ◽  
pp. 23-30 ◽  
Author(s):  
Najwa A. Rashid ◽  
Sujata Lalitkumar ◽  
Parameswaran G. Lalitkumar ◽  
Kristina Gemzell-Danielsson
Keyword(s):  
Human Embryo ◽  
Embryo Implantation ◽  
Endometrial Receptivity
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