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

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.

Download Full-text

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

Journal of the Endocrine Society ◽

10.1210/jendso/bvaa046.576 ◽

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.

Download Full-text

Therapeutic Approaches and Role of ncRNAs in Cardiovascular Disorders and Insulin Resistance

BioMed Research International ◽

10.1155/2017/4078346 ◽

2017 ◽

Vol 2017 ◽

pp. 1-10 ◽

Cited By ~ 8

Author(s):

Kalupahana Irushi Pamodya Liyanage ◽

Gamage Upeksha Ganegoda

Keyword(s):

Gene Expression ◽

Insulin Resistance ◽

Cardiovascular Diseases ◽

Gene Expression Regulation ◽

Therapeutic Approaches ◽

Gene Expressions ◽

Diagnostic Biomarkers ◽

Cellular Processes ◽

Regulatory Functions

Diseases resulting from alterations in gene expressions through mutations in the genes or through changes in the gene expression regulation could be identified through the analysis of RNA expressions. ncRNAs play a significant role in regulation of the gene expression by controlling the expression levels of the coding RNAs and other cellular processes. Discoveries have shown that the human genome is encoded with sequences responsible for the transcription of thousands of ncRNAs. Even though the studies conducted on ncRNAs are still at initial stages, facts established so far display biomarkers that confirm their relationship with certain diseases such as cancers, cardiovascular diseases, and insulin resistance. These studies have been facilitated with high throughput modern sequencing techniques such as microarrays and RNA sequencing. The data obtained through the above analysis are processed with the aid of existing databases, to deduce conclusions on different diagnostic biomarkers and therapeutic targets for specific diseases. This review focuses on the association of ncRNAs in disease prediction, focusing mainly on cardiovascular diseases and disorders caused by insulin resistance. The report also analyzes regulatory functions of ncRNAs and novel approaches used in disease therapeutics.

Download Full-text

3α-Hydroxysteroid Dehydrogenase Type III Deficiency: A Novel Mechanism for Hirsutism

The Journal of Clinical Endocrinology & Metabolism ◽

10.1210/jc.2007-2708 ◽

2008 ◽

Vol 93 (4) ◽

pp. 1298-1303 ◽

Cited By ~ 4

Author(s):

Anne Z. Steiner ◽

Lilly Chang ◽

Qing Ji ◽

Murad Ookhtens ◽

Andrew Stolz ◽

...

Keyword(s):

Gene Expression ◽

Hydroxysteroid Dehydrogenase ◽

Conversion Ratio ◽

City Hospital ◽

Relative Expression ◽

Tissue Levels ◽

Type Iii ◽

Normal Women ◽

Relative Gene

Abstract Context: Dihydrotestosterone (DHT), the primary active androgen in peripheral target tissues, is metabolized by 3α-hydroxysteroid dehydrogenase type III (3α-HSD), encoded by the AKR1C2 gene, forming 5α-androstane-3α,17β-diol (3α-diol). 3α-HSD may play a role in the pathogenesis of hirsutism. Objectives: Our objective was to evaluate the role of 3α-HSD in hirsutism by comparing 1) tissue levels of active androgens, 2) relative gene expression of AKR1C2, and 3) activity of 3α-HSD in genital skin from normal and hirsute women. Design: Genital skin was obtained from normal and hirsute women. After homogenization, testosterone (T) and DHT levels were quantified by conventional RIA. From isolated RNA, relative expression of AKR1C2 was determined by real-time PCR. In addition, minced genital skin was incubated with [3H]DHT, and the product, [3H]3α-diol, was quantified by radio-HPLC. Setting: The study took place at an inner-city hospital. Patients: Patients included women undergoing posterior colporrhaphy. Main Outcome Measures: We assessed 1) tissue levels of T, DHT, and 3α-diol; 2) relative expression of AKR1C2; and 3) conversion ratio of [3H]3α-diol to [3H]DHT. Results: In genital skin, tissue DHT and T concentrations in hirsute women were 1.90-fold and 1.84-fold higher than in normal women (P =0 .002 and 0.03), and relative expression of AKR1C2 mRNA was reduced approximately 7-fold (P = 0.04). Genital skin from hirsute women showed less metabolism of [3H]DHT to [3H]3α-diol (conversion ratio, 0.24 ± 0.19 vs. 0.85 ± 0.55, P = 0.01). Conclusions: In genital skin of hirsute women, reduced AKR1C2 gene expression and 3α-HSD activity results in decreased DHT metabolism and elevated tissue levels of DHT. Diminished DHT metabolism may play an important role in the pathogenesis of hirsutism.

Download Full-text

Pesticide application has little influence on coding and non-coding gene expressions in rice

10.21203/rs.2.9415/v1 ◽

2019 ◽

Author(s):

Sajid Muhammad ◽

Jingai Tan ◽

Pingchuan Deng ◽

Tingting Li ◽

Haohua He ◽

...

Keyword(s):

Gene Expression ◽

Potential Role ◽

Insect Pests ◽

Host Gene Expression ◽

Pesticide Application ◽

Gene Expressions ◽

Number Of Genes ◽

Non Coding Rnas ◽

Transcriptomic Changes

Abstract Background Agricultural insects are one of the major threats to crop yield. It is a known fact that pesticide application is an extensive approach to eliminate insect pests, and has severe adverse effects on environment and ecosystem; however, there is lack of knowledge whether it could influence the physiology and metabolic processes in plants. Results Here, we systemically analyzed the transcriptomic changes in rice after a spray of two commercial pesticides, Abamectin (ABM) and Thiamethoxam (TXM). We found only a limited number of genes were altered by two pesticide applications, indicating that pesticides cannot dramatically affect the performance of rice. Nevertheless, we characterized some Differentially Expressed Genes (DEGs) and long non-coding RNAs (lncRNAs) that can be impacted by both two pesticides, suggesting their certain involvement in response to farm chemicals. Moreover, we detected several alternative splicing (AS) alterations accompanied by host gene expression, illustrating a potential role of AS in control of gene transcription during insecticide spraying. Finally, a couple of transposons were identified significantly changed with pesticides treatment, leading to a variation in adjacent coding or non-coding transcripts. Conclusions Altogether, our results provide valuable insights into pest management through appropriate timing and balanced mixture over sustainable application of field drugs.

Download Full-text

Cellular heterogeneity and MTH1 play key roles in galactose mediated signaling of the GAL switch to utilize the disaccharide melibiose

10.1101/2021.06.16.448739 ◽

2021 ◽

Author(s):

Rajesh Kumar Kar ◽

Paike Jayadeva Bhat

Keyword(s):

Gene Expression ◽

Glucose Repression ◽

Expression Patterns ◽

Negative Regulator ◽

Cellular Heterogeneity ◽

Growth Defect ◽

Gene Expressions ◽

Gal1 Promoter ◽

Mel Gene

Yeast metabolizes the disaccharide melibiose by hydrolyzing it into equimolar concentrations of glucose and galactose by MEL1-encoded α-galactosidase. Galactose metabolizing genes (including MEL1) are induced by galactose and repressed by glucose, which are the products of melibiose hydrolysis. Therefore, how melibiose catabolization and utilization take place by circumventing the glucose repression is an enigma. Other than the galactose metabolizing genes MTH1, a negative regulator of glucose signal pathway has Gal4p binding sites and is induced by galactose and repressed by high glucose concentration. But, at low or no glucose MTH1 along with its paralogue STD1 represses hexose transporters, that are involved in glucose transport. This sort of tuning of glucose and galactose regulation motivated us to delineate the role of MTH1 as a regulator of MEL1 expression and melibiose utilization. The deletion mutant of MTH1 shows growth defect on melibiose and this growth defect is enhanced upon the deletion of both MTH1 and its paralogue STD1. Microscopy and flowcytometry analysis, suggest, that even though MEL1 and GAL1 promoter are under Gal4p and Gal80p regulation, upon deletion of MTH1 it hampers only MEL1 expression, but not the GAL1 gene expression. By using 2-Deoxy galactose toxicity assay, we observed phenotypic heterogeneity in cells grown on melibiose i.e. after cleaving of melibiose a fraction of cell population utilizes glucose and another fraction utilizes galactose and coexist together. Understanding GAL/MEL gene expression patterns in melibiose will have great implication to understand various other complex sugar utilizations, tunable gene expressions and complex feedback gene regulations.

Download Full-text

Role of Cdx-2 in insulin and proglucagon gene expression: a study using the RIN-1056A cell line with an inducible gene expression system

Journal of Endocrinology ◽

10.1677/joe.1.06152 ◽

2005 ◽

Vol 186 (1) ◽

pp. 179-192 ◽

Cited By ~ 3

Author(s):

Yi Zhao ◽

Tao Liu ◽

Nina Zhang ◽

Fenghua Yi ◽

Qinghua Wang ◽

...

Keyword(s):

Gene Expression ◽

Cell Line ◽

Cell Lines ◽

Expression System ◽

Insulin Gene ◽

Luciferase Reporter ◽

Luciferase Reporter Gene ◽

Gene Expressions ◽

Insulin Gene Expression

Although the homeobox gene Cdx-2 was initially isolated from the pancreatic β cell line HIT-T15, no examination of its role in regulating endogenous insulin gene expression has been reported. To explore further the role of Cdx-2 in regulating both insulin and proglucagon gene expression, we established an ecdysone-inducible Cdx-2 expression system. This report describes a study using the rat insulinoma cell line RIN-1056A, which abundantly expresses both insulin and proglucagon (glu), and relatively high amounts of endogenous Cdx-2. Following the introduction of the inducible Cdx-2 expression system into this cell line and the antibiotic selection procedure, we obtained novel cell lines that displayed dramatically reduced expression of endogenous Cdx-2, in the absence of the inducer. These novel cell lines did not express detectable amounts of glu mRNA or the glucagon hormone, while their insulin expression was not substantially affected. In the presence of the inducer, however, transfected Cdx-2 expression was dramatically increased, accompanied by stimulation of endogenous Cdx-2 expression. More importantly, activated Cdx-2 expression was accompanied by elevated insulin mRNA expression, and insulin synthesis. Cdx-2 bound to the insulin gene promoter enhancer elements, and stimulated the expression of a luciferase reporter gene driven by these enhancer elements. Furthermore, Cdx-2 and insulin gene expressions in the wild-type RIN-1056A cells were stimulated by forskolin treatment, and forskolin-mediated activation on insulin gene expression was attenuated in the absence of Cdx-2. We suggest that Cdx-2 may mediate the second messenger cAMP in regulating insulin gene transcription.

Download Full-text

Epitranscriptomics: A New Layer of microRNA Regulation in Cancer

Cancers ◽

10.3390/cancers13133372 ◽

2021 ◽

Vol 13 (13) ◽

pp. 3372

Author(s):

Veronica De Paolis ◽

Elisa Lorefice ◽

Elisa Orecchini ◽

Claudia Carissimi ◽

Ilaria Laudadio ◽

...

Keyword(s):

Gene Expression ◽

Potential Role ◽

Fine Tuning ◽

Cancer Development ◽

Transcriptional Level ◽

Rna Modifications ◽

Gene Expressions ◽

Microrna Regulation ◽

Non Coding Rnas

MicroRNAs are pervasive regulators of gene expression at the post-transcriptional level in metazoan, playing key roles in several physiological and pathological processes. Accordingly, these small non-coding RNAs are also involved in cancer development and progression. Furthermore, miRNAs represent valuable diagnostic and prognostic biomarkers in malignancies. In the last twenty years, the role of RNA modifications in fine-tuning gene expressions at several levels has been unraveled. All RNA species may undergo post-transcriptional modifications, collectively referred to as epitranscriptomic modifications, which, in many instances, affect RNA molecule properties. miRNAs are not an exception, in this respect, and they have been shown to undergo several post-transcriptional modifications. In this review, we will summarize the recent findings concerning miRNA epitranscriptomic modifications, focusing on their potential role in cancer development and progression.

Download Full-text

Role of small nuclear RNAs in eukaryotic gene expression

Essays in Biochemistry ◽

10.1042/bse0540079 ◽

2013 ◽

Vol 54 ◽

pp. 79-90 ◽

Cited By ~ 34

Author(s):

Saba Valadkhan ◽

Lalith S. Gunawardane

Keyword(s):

Gene Expression ◽

Protein Interactions ◽

Rna Stability ◽

Splice Sites ◽

Branch Site ◽

Small Nuclear Rnas ◽

Eukaryotic Gene Expression ◽

Eukaryotic Gene ◽

Rna Biogenesis

Eukaryotic cells contain small, highly abundant, nuclear-localized non-coding RNAs [snRNAs (small nuclear RNAs)] which play important roles in splicing of introns from primary genomic transcripts. Through a combination of RNA–RNA and RNA–protein interactions, two of the snRNPs, U1 and U2, recognize the splice sites and the branch site of introns. A complex remodelling of RNA–RNA and protein-based interactions follows, resulting in the assembly of catalytically competent spliceosomes, in which the snRNAs and their bound proteins play central roles. This process involves formation of extensive base-pairing interactions between U2 and U6, U6 and the 5′ splice site, and U5 and the exonic sequences immediately adjacent to the 5′ and 3′ splice sites. Thus RNA–RNA interactions involving U2, U5 and U6 help position the reacting groups of the first and second steps of splicing. In addition, U6 is also thought to participate in formation of the spliceosomal active site. Furthermore, emerging evidence suggests additional roles for snRNAs in regulation of various aspects of RNA biogenesis, from transcription to polyadenylation and RNA stability. These snRNP-mediated regulatory roles probably serve to ensure the co-ordination of the different processes involved in biogenesis of RNAs and point to the central importance of snRNAs in eukaryotic gene expression.

Download Full-text