scholarly journals MON-008 Estrogen-Responsive and -Unresponsive Gene Expressions Promoted by Enhancers Specifically Hypomethylated in Endometriotic Cells May Become a Molecular Marker in Endometriosis Lesions

2020 ◽  
Vol 4 (Supplement_1) ◽  
Author(s):  
Masao Izawa ◽  
Yukihiro Azuma ◽  
Naohiro Hori ◽  
Fuminori Taniguchi ◽  
Tasuku Harada
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
In Silico ◽  
Premenopausal Women ◽  
Institutional Review Boards ◽  
Gene Expressions ◽  
Relative Expression ◽  
Endometrial Cells ◽  
Comparable Level ◽  
Active Enhancer

Abstract BACKGROUND: Endometriosis is an estrogen-dependent, inflammatory disease, and the role of estrogen is obvious because the symptoms associated with endometriosis often disappear after menopause, and GnRH agonists or progestin relieve the pelvic lesions and endometriosis-associated pain. However, there are limitations to these treatments that target the estrogen reduction in endometriotic lesions. We sought to define an aberrant gene expression derived from an epigenetic background in endometriosis.Objective: In the hope of overcoming the limitations of endocrine treatments in endometriosis, we examined estrogen receptor (ER)-dependent and -independent gene expressions promoted by active enhancers specifically hypomethylated in endometriotic cells. Patients: Institutional Review Boards approved this project. We obtained the informed consent from all patients. The chocolate cyst lining in ovaries of patients with endometriosis was the source of endometriotic tissue. As the control, the eutopic endometrial tissues were obtained from uteri of premenopausal women who had uterine leiomyoma.Methods: Stromal cells were prepared from endometriotic and endometrial tissues. Gene expression was examined using RT-PCR. The potential function of hypomethylated gene sequence as an active enhancer was evaluated by ChIP analysis using anti-H3K4me1 and anti-H3K27ac antibodies and eRNA expression analysis. Using ChIP-seq and ChIA-PET analysis in silico, ER-specific loci within gene bodies and the up- and downstream regions were extracted. ER-dependent gene expression was examined using estradiol or SERM.Results: ER expression in endometriotic cells.1) Relative expression of ERα mRNA was estimated to be one tenth of that in endometrial cells. 2) Relative expression of ERβ1 mRNA was 40-fold higher than that in endometrial cells, which is at a comparable level of the ERα. 3) ERβ2 mRNA expression was at a comparable level of the ERβ1. From our DNA methylation and gene expression analysis, 6 genes were selected and classified into 3 categories: estrogen-responsive genes with specific methylation (ESR1 and ESR2) or without any methylation (TGFα and GREB1), and estrogen-unresponsive but upregulated genes depending on specific hypomethylation (GATA6 and CYP19). 4) ChIP-seq and ChIA-PET analysis in silico suggested the presence of ER-specific loci within gene bodies and the up- and downstream in estrogen-responsive genes. 5) ChIP and eRNA expression analysis predicted active enhancer regions both in estrogen-responsive and -unresponsive genes. 6) In response to estrogen, TGFα and GREB1 expressions were upregulated, but ESR1 and ESR2 showed marginal responses.Conclusion: We focused on estrogen-responsive and -unresponsive genes linked to the epigenetic environment of endometriotic lesions, and revealed a facet of gene expression in endometriotic cells.

scholarly journals Molecular Background of Estrogen-Dependent and -Independent Gene Expressions in Endometriotic Lesions

2021 ◽  
Vol 5 (Supplement_1) ◽  
pp. A770-A770
Author(s):  
Masao Izawa ◽  
Yukihiro Azuma ◽  
Fuminori Taniguchi ◽  
Tasuku Harada
Keyword(s):  
Gene Expression ◽  
Specific Primer ◽  
Gene Expressions ◽  
Relative Expression ◽  
Endometrial Cells ◽  
Comparable Level ◽  
Independent Gene ◽  
Active Enhancer ◽  
Primer Sets

Abstract Background: Endometriosis is an estrogen-dependent disease, and the role of estrogen is obvious because the symptoms associated with endometriosis often disappear after menopause, and GnRH agonists or progestin relieve the pelvic lesions and endometriosis-associated pain. However, there are limitations to these treatments that target the estrogen reduction in endometriotic lesions. As a possible background, we hypothesized a role of the local environment with high estrogen depending on aromatase upregulation in endometriotic lesions. Objective: To test our hypothesis, we re-evaluated the expression profile of estrogen receptor (ER), and then searched for the estrogen-dependent gene expressions in endometriotic cells. Finally, we approached the epigenetic background of gene expressions in endometriotic cells. Patients: Institutional Review Boards approved this project. We obtained the informed consent from all patients. The chocolate cyst lining in ovaries of patients with endometriosis was the source of endometriotic tissue. As the control, the eutopic endometrial tissues were obtained from uteri of premenopausal women who had uterine leiomyoma. Methods: Stromal cells were prepared from endometriotic and endometrial tissues. Gene expression was evaluated using RT-PCR. Specific primer sets of unique 5’-UTR exons/exon 2 in ESR1 and specific primer sets of unique 5’-UTR exons/exon1 in ESR2 were used for the analysis of promoter usage. Primer sets of exon 7 and exon 8 in ESR2 were used to evaluate the expression of ERβisoform. Using SERM(PPT and DPN), ER-dependent gene expression was estimated. The potential function of hypomethylated gene sequence as an active enhancer was evaluated by ChIP analysis and eRNA expression. Results: 1) Relative expression of ERα mRNA in endometriotic cells was estimated to be one tenth of that in endometrial cells. 2) Relative expression of ERβ1 mRNA was 40-fold higher than that in endometrial cells, which is almost at a comparable level of the ERα. 3) In addition to ERβ1 mRNA, a splice variant ERβ2 was expressed at a comparable level of the ERβ1. 4) Top ten genes, up- or down-regulated in response to SERM, were extracted in endometriotic cells. 5) TGFA expression was upregulated at a comparable level in response to PPT and DPN. 6) A stretch of hypomethylated sequence, which includes an ERE at 50kb upstream from the TSS, was suggested as active enhancer. 7) ESR1 and ESR2showed a marginal response to SERM. 8) GATA6 and CYP19 were highly expressed in endometriotic cells, and hypomethylated sequences in these genes were suggested as active enhancer. Conclusion: In the hope of overcoming the limitations of endocrine treatments in endometriosis, we examined ER-dependent and -independent gene expressions using endometriotic cells. The results suggest one aspect of gene expression in endometriosis lesions.

Molecular cloning, gene expression analysis, and in silico characterization of UDP‐N‐acetylglucosamine pyrophosphorylase from Bombyx mori

2019 ◽  
Vol 66 (5) ◽  
pp. 880-899
Author(s):  
Bhagath Kumar Palaka ◽  
Anbumani Velmurugan Ilavarasi ◽  
Tuleshwori Devi Sapam ◽  
Kasi Viswanath Kotapati ◽  
Venkata Satyanarayana Nallala ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bombyx Mori ◽  
Molecular Cloning ◽  
Expression Analysis ◽  
In Silico ◽  
Gene Expression Analysis ◽  
In Silico Characterization

scholarly journals An Integrated Preprocessing Approach for Exploring Single-Cell Gene Expression in Rare Cells

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Junyi Shang ◽  
David Welch ◽  
Manuela Buonanno ◽  
Brian Ponnaiya ◽  
Guy Garty ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Bystander Effect ◽  
Kinase Inhibitor ◽  
Digital Pcr ◽  
Lung Fibroblasts ◽  
Gene Expressions ◽  
Rare Cells

AbstractExploring the variability in gene expressions of rare cells at the single-cell level is critical for understanding mechanisms of differentiation in tissue function and development as well as for disease diagnostics and cancer treatment. Such studies, however, have been hindered by major difficulties in tracking the identity of individual cells. We present an approach that combines single-cell picking, lysing, reverse transcription and digital polymerase chain reaction to enable the isolation, tracking and gene expression analysis of rare cells. The approach utilizes a photocleavage bead-based microfluidic device to synthesize and deliver stable cDNA for downstream gene expression analysis, thereby allowing chip-based integration of multiple reactions and facilitating the minimization of sample loss or contamination. The utility of the approach was demonstrated with QuantStudio digital PCR by analyzing the radiation and bystander effect on individual IMR90 human lung fibroblasts. Expression levels of the Cyclin-dependent kinase inhibitor 1a (CDKN1A), Growth/differentiation factor 15 (GDF15), and Prostaglandin-endoperoxide synthase 2 (PTGS2) genes, previously shown to have different responses to direct and bystander irradiation, were measured across individual control, microbeam-irradiated or bystander IMR90 cells. In addition to the confirmation of accurate tracking of cell treatments through the system and efficient analysis of single-cell responses, the results enable comparison of activation levels of different genes and provide insight into signaling pathways within individual cells.

scholarly journals In silico gene expression analysis reveals glycolysis and acetate anaplerosis in IDH1 wild-type glioma and lactate and glutamate anaplerosis in IDH1-mutated glioma

Oncotarget ◽  
2017 ◽  
Vol 8 (30) ◽  
pp. 49165-49177 ◽  
Author(s):  
Mohammed Khurshed ◽  
Remco J. Molenaar ◽  
Krissie Lenting ◽  
William P. Leenders ◽  
Cornelis J.F. van Noorden
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
In Silico ◽  
Gene Expression Analysis ◽  
Wild Type

scholarly journals Some aspects of metal ion transport and in silico gene expression analysis of potassium/sodium ion transporters, channels and exchangers in root nodules

2021 ◽  
Vol 66 (1) ◽  
Author(s):  
Natalia Trifonova ◽  
Maria Koroleva ◽  
Elena Fedorova
Keyword(s):  
Gene Expression ◽  
Ion Transport ◽  
Expression Analysis ◽  
In Silico ◽  
Metal Ion ◽  
Gene Expression Analysis ◽  
Root Nodule ◽  
Root Nodules ◽  
Sodium Ion ◽  
Metal Ion Transport

Rhizobia establish a symbiotic relationship with legumes, which results in the formation of root nodules, the ecological niche for intracellular rhizobia. The infected cell of a root nodule is a special integral unit of plant and nitrogen fixing rhizobia. Nodules tend to be very sensitive to ionic stresses, such as salt stress. High vulnerability toward ionic stresses might be due to defects in ion balance and transport in the infected tissue. The purpose of this minireview is to summarize the current data regarding metal ion transport in the root nodule, with particular emphasis on potassium/sodium ion transport. A bioinformatic approach and in silico gene expression analysis have been used to obtain some insight for K+/Na+ transportеr channels and exchangers in root nodule developmental zones.

307 MATURATION RATE AND GENE EXPRESSION ANALYSIS OF GOAT OOCYTES SELECTED BY FOLLICLE SIZE AND BRILLIANT CRESYL BLUE STAINING

2015 ◽  
Vol 27 (1) ◽  
pp. 242
Author(s):  
M. Yang ◽  
S. Hu ◽  
L. Cox ◽  
M. Regouski ◽  
H. Rutigliano ◽  
...  
Keyword(s):  
Gene Expression ◽  
Oocyte Maturation ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Oocyte Quality ◽  
Developmental Competence ◽  
Brilliant Cresyl Blue ◽  
Relative Expression ◽  
Cresyl Blue ◽  
Maturation Rate

Oocyte quality plays a critical role in determining the success of embryo development. Studies on cattle and goats indicate that oocytes derived from large follicles (LFO) have greater developmental competence than those derived from small follicles (SFO). Brilliant cresyl blue (BCB) staining determines the activity of glucose-6-phosphate dehydrogenase and is a commonly used noninvasive marker of oocyte competence. Studies in pigs, goats, cows, mice, and dogs showed that the maturation and blastocyst developmental rate of BCB+ oocytes is significantly higher than BCB– oocytes. The aim of this study was to evaluate the maturation rate of goat oocytes selected based on follicular size and BCB staining and compare their relative patterns of gene expression. Maturation rate and gene expression profile were expected to be different in these oocyte groups. Cumulus-oocyte complexes were recovered from abattoir-derived ovaries using a slicing technique. Eleven rounds of oocyte maturation and 4 rounds of BCB staining were carried out. During each replicate, oocytes from large (≥3 mm) and small (<3 mm) follicles were collected separately from the same group of ovaries. Oocyte maturation rates were 54.3 ± 5.4% for LFO (n = 378) and only 33.5 ± 3.7% for SFO (n = 981; P < 0.01). The BCB+ (n = 223) oocytes yielded a significantly higher maturation rate than the BCB– (n = 194) oocytes (56.1 ± 1.8 v. 20.6 ± 3.8%, respectively; P < 0.001). Gene expression analysis was conducted on individual MII oocytes (21 oocytes per group). Specific target amplification was performed on a single oocyte directly by using the CellsDirect One-Step qRT–PCR Kit (Invitrogen). Quantitative real-time PCR was then performed using the 48.48 BioMark platform from Fluidigm. Forty two genes were selected from the following categories: growth factors, transcription factors, metabolism, pluripotency, cell cycle, apoptosis, and oocyte-specific genes. Relative expression values were calculated using the ΔΔCT (fold change) method and analysed by ANOVA. The significance was assigned at P < 0.05. The relative expression of CCNA2, CDK2, CCNB1, POU5F1, SOX2, EGF, FGF2, GDF9, ZP3, BCL2, GJA1, DDR1, PFKFB3, IGF2R, and GRB10 was significantly greater (P < 0.05) in both LFO and BCB+ oocytes compared to SFO and BCB– oocytes, respectively. The proapoptotic gene BAX, the ACSL3 gene involved in fatty acid oxidation, and the growth factor IGF1 were expressed significantly higher (P < 0.05) in SFO compared to LFO. By investigating these differentially expressed transcripts, we will better understand pathways involved in oocyte developmental competence and potentially use them as markers of oocyte quality. We expect that the ability to select oocytes of better quality based on BCB staining will improve outcomes of IVF and SCNT.

In silico identification of an epithelial core signature in human tumors.

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. 10628-10628
Author(s):  
Chirayu Pankaj Goswami ◽  
Oscar D. Cano ◽  
Yesim Gokmen-Polar ◽  
Sunil S. Badve
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Expression Analysis ◽  
In Silico ◽  
Differential Expression Analysis ◽  
Gene Signature ◽  
Venn Diagram ◽  
Expression Data ◽  
Tissue Samples ◽  
Gene Probes

10628 Background: Gene expression analysis is performed on grossly selected specimens often without any microscopic analysis of tumor content. In studies where histological analyses have been performed, cases having 80% or more tumor content are used for microarray analysis. The variability in amount of epithelial and stromal cells may generate to misleading differential expression analysis and selection for wrong targets for therapeutics. It is also often unclear, whether the genes identified are stromal or epithelial in origin. The goal of this study was to identify genes that define core epithelial phenotype; these genes could provide means of normalization of expression data. Methods: The CABIG GSK microarray (HG-U133_plus_2) data consisting of 950 cell lines from carcinoma (n=562), non-carcinoma (n=385) and normal tissue (n=3) was analyzed to identify epithelial specific genes. 10 carcinomas each from 11 sites (n=110) and an equal number of non-carcinomas were randomly selected. In silico analyses were performed by 1) identifying genes differentially expressed between carcinoma and non-carcinoma samples using a one way ANOVA; 2) identifying gene signature associated with carcinoma using Predictive Analysis of Microarrays (PAM) and 3) a weighted gene coexpression network analysis (WGCNA) was performed to identify co-expression modules. A similar analysis was also performed on tissue samples (E-GEOD-12360) from carcinomas and non-carcinomas. Venn-diagram was generated to identify intersecting set. Results: Comparison of the carcinoma and non-carcinoma samples using ANOVA identified 1455 differential expressed gene probes in cell lines and 540 gene probes in tissues (FDR=1E-10). The cell lines analysis identified 5 modules and a 65-gene signature (43 core and 22 accessory set) that was specific for epithelial cells. In the tissue analysis a 188-gene signature was similarly identified. Cross-comparison identified a smaller 31 gene intersecting set; this was not associated with loss of discriminatory power. Conclusions: A 31 geneset which can be used to determine the epithelial content of heterogeneous tumors, was identified. This study has the potential to significantly impact the use of microarray based gene expression data.

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