Expression data from Drosophila S2* cells treated with the steroid hormone 20-hydroxy-ecdysone (20E)
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ABSTRACT:
ORGANISM(S): Drosophila melanogaster
SUBMITTER: Thomas Flatt
PROVIDER: E-GEOD-46020 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Previously we and other teams have found that 20E modulates the induction and expression of antimicrobial peptides (AMPs) in immune-challenged Drosophila cell culture or whole animals. To identify potential downstream targets of 20E involved in modulating the immune response we used Affymetrix gene chips (microarrays) to compare the transcriptomes of Drosophila S2* cells treated or not with 20E for 24 hours.
2013-04-13 | GSE46020 | GEO
Project description:Juvenile hormone (JH) and 20-hydroxy-ecdysone (20E) are highly versatile hormones, coordinating development, growth, and reproduction in insects. Pulses of 20E provide key signals for initiating developmental and physiological transitions, while JH promotes or inhibits these signals in a stage-specific manner. Previous evidence suggests that JH and 20E might modulate innate immunity, but whether and how these hormones interact to regulate the immune response remains unclear. Here we show that JH and 20E have antagonistic effects on the expression of antimicrobial peptides (AMPs) in Drosophila melanogaster. In S2* cells challenged with bacterial peptidoglycans, 20E induces promoter activity and expression of AMPs in a dose-dependent manner, while JH III and its synthetic analogs (JHa) methoprene and pyriproxyfen abolish this 20E-dependent response. Using microarrays and GFP reporter gene assays in adult flies, we confirm that JH is a hormonal immuno-suppressor in vivo. When silencing both partners of the ecdysone receptor (EcR ) / ultraspiracle (USP) heterodimer with RNAi in S2* cells, 20E fails to activate Diptericin (Dpt) expression, suggesting that 20E regulates expression of this gene through EcR / USP signaling. In contrast, silencing methoprene-tolerant (MET), a candidate JH receptor, does not impair the immuno-suppressive action of JH III and JHa, indicating that in this context MET does not function as a JH receptor. Our results suggest that the balance of 20E and JH is a major determinant of immune homeostasis in insects. Experiment Overall Design: To examine the transcriptional response of y, w flies to treatment with exogenous JH, we performed a microarray experiment on females treated with JH or solvent (control). Flies were grown on regular yeast diet, switched to no-yeast food within one hour of eclosion, and yeast-starved for 5 days posteclosion to lower their endogenous JH titer and to synchronize their physiology (cf. Tu and Tatar, 2003; Gershman et al., 2007). Subsequently, we anesthetized flies on ice and topically treated them with 0.1 ïl of 187 mM JH III in acetone or with 0.1ï ïl 100% acetone (control) using a 1 ïl Hamilton syringe with a repeating dispenser. 12 hours after hormone administration, samples were snap-frozen in liquid nitrogen and stored at -80°C. RNA was isolated from samples (2 JH samples, 2 control samples, each with 30 females) by lysis, as described in Gershman et al. (2007). cDNA products were hybridized at the Brown University Genomics Core Facility to Affymetrix GeneChip Drosophila_1 Genome Arrays (2 replicate chips per treatment). The dataset consisted of 14,009 probe sets, with 6,142 probe sets annotated. Expression data were analyzed for significant over- or underrepresentation of gene ontology (GO) terms with the web application FatiGO (Al-Shahrour et al., 2004), using a two-fold change criterion. To test whether JH treatment significantly suppresses expression of AMPs we used t-tests implemented in JMP IN 5.1.
2008-06-16 | E-GEOD-9001 | biostudies-arrayexpress
Project description:To identify 20E-regulated genes, wandering third instar larvae were dissected and their organs were cultured in the presence of either no hormone, 20E alone, cycloheximide alone, or 20E plus cycloheximide for six hours. Experiment Overall Design: Eight partial blue gut third instar larvae were dissected in each well of a 9 well glass dish (Corning) and cultured in ~100 µl oxygenated Schneiders Drosophila Medium (Gibco) at 25°C. Cultures were incubated in an a styrofoam box under a constant flow of oxygen. Following an initial incubation of 1 hour, the medium was removed and replaced with either fresh Schneiders Drosophila Medium (no hormone), medium plus 8.5x10-5 M cycloheximide (Sigma), medium plus 5x10-6 M 20-hydroxyecdysone (Sigma), or medium plus cycloheximide and 20E, each for 6 hrs at 25°C. Organs were collected and RNA extracted from these samples was analyzed on Affymetrix Drosophila Genome Arrays.
2007-10-31 | E-GEOD-3060 | biostudies-arrayexpress
Project description:Juvenile hormone (JH) and 20-hydroxy-ecdysone (20E) are highly versatile hormones, coordinating development, growth, and reproduction in insects. Pulses of 20E provide key signals for initiating developmental and physiological transitions, while JH promotes or inhibits these signals in a stage-specific manner. Previous evidence suggests that JH and 20E might modulate innate immunity, but whether and how these hormones interact to regulate the immune response remains unclear. Here we show that JH and 20E have antagonistic effects on the expression of antimicrobial peptides (AMPs) in Drosophila melanogaster. In S2* cells challenged with bacterial peptidoglycans, 20E induces promoter activity and expression of AMPs in a dose-dependent manner, while JH III and its synthetic analogs (JHa) methoprene and pyriproxyfen abolish this 20E-dependent response. Using microarrays and GFP reporter gene assays in adult flies, we confirm that JH is a hormonal immuno-suppressor in vivo. When silencing both partners of the ecdysone receptor (EcR ) / ultraspiracle (USP) heterodimer with RNAi in S2* cells, 20E fails to activate Diptericin (Dpt) expression, suggesting that 20E regulates expression of this gene through EcR / USP signaling. In contrast, silencing methoprene-tolerant (MET), a candidate JH receptor, does not impair the immuno-suppressive action of JH III and JHa, indicating that in this context MET does not function as a JH receptor. Our results suggest that the balance of 20E and JH is a major determinant of immune homeostasis in insects. Keywords: Topical hormone treatment of whole flies
2007-12-31 | GSE9001 | GEO
Project description:Goblet cell numbers decrease within the conjunctival epithelium in drying and cicatrizing ocular surface diseases. Factors regulating goblet cell differentiation in conjunctival epithelium are unknown. Recent data indicate that the transcription factor SAM-pointed domain epithelial-specific transcription factor (Spdef) is essential for goblet cell differentiation in tracheobronchial and gastrointestinal epithelium of mice. Using Spdef -/- mice, we determined that Spdef is required for conjunctival goblet cell differentiation and that Spdef -/- mice, which lack conjunctival goblet cells, have significantly increased corneal surface fluorescein staining and tear volume, a phenotype consistent with dry eye. Microarray analysis of conjunctival epithelium in Spdef -/- mice identified 43 signficantly upregulated genes and 110 signficantly downregulated genes in the conjunctival epithelium of Spdef -/- mice compared to that of Spdef +/+ control mice (3 fold change, p<0.01). Downregulated genes of particular interested included goblet cell-specific genes (Muc5ac, Tff1, Gcnt3). Upregulated genes included epithelial cell differentiation/keratinization genes (Sprr2h, Tgm1) and pro-inflammatory genes (Il1-α, Il-1β, Tnf-α), all of which are upregulated in dry eye. Interestingly, four Wnt pathway genes were downregulated. Conjunctival epithelium of Spdef +/+ and Spdef -/- mice was collected by laser capture microdissection for RNA extraction and hybridization on Affymetrix microarrays to determine if gene expression patterns in the conjunctival epithelium of Spdef -/- mice is altered compared to that of Spdef +/+ mice.
2013-02-08 | E-GEOD-44101 | biostudies-arrayexpress
Project description:We have develped a novel method of making siRNAs (named pro-siRNA for prokaryotic siRNA). To evaluate off-targeting of pro-siRNA, we compared mRNA expression profile of HeLa-d1EGFP cells transfected with 4 nM LMNA siRNAs and pro-siRNAs by microarray. We used microarray to study off-target effect of siRNAs in HeLa-d1EGFP cell line. After transfection of siRNAs for 24 hrs, RNA were extracted using Trizol. RNA samples were sent to Microarray Core at Dana-Farber Cancer Institute (http://macf-web.dfci.harvard.edu/index.php?option=com_frontpage&Itemid=1) to be probed using Human Gene 1.0 ST (Affymetrix).
2013-02-06 | E-GEOD-44105 | biostudies-arrayexpress
Project description:Kc167 cells were mock-treated/treated with combinations of steroid hormone ecdysone and gamma-irradiation, and harvested. The expression profiles were determined using Affymetrix Drosophila Genechip 1 arrays. Comparisons between the sample groups allow the identification of genes with ecdysone- and/or radiation-responsive expression patterns. Experiment Overall Design: 1 set of control, ecdysone, gamma-irradiated, ecdysone + irradiated samples was analyzed.
2008-06-12 | E-GEOD-3072 | biostudies-arrayexpress
Project description:Glycolytic Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) catalyzes the conversion of glyceraldehyde 3-phospate to 1,3-bisphosphoglycerate by coupling with the reduction of NAD+ to NADH. We generated mutants of the Arabidopsis plastidial GAPDH isoforms (At1g79530, At1g16300; GAPCp1, GAPCp2). gapcp double mutants (gapcp1 gapcp2) display a drastic phenotype of arrested root development and sterility.Complex interactions occurring between ABA and sugar signal transduction pathways have been shown, but the molecular mechanisms connecting both pathways are not well understood. Since we found drastic carbohydrate changes in gapcp1 gapcp2, we studied their response to ABA. by performing a microarray analysis comparing gapcp1 gapcp2 and wild type seedlings after a long term treatment with ABA. 15-day old Arabidopsis seedlings (Col 0) and gapcp1gapcp2 double mutants were used for RNA extraction and hybridization on Affymetrix microarrays.
2010-05-28 | E-GEOD-21765 | biostudies-arrayexpress
Project description:Steroid hormones act as important developmental switches and their nuclear receptors regulate many genes. However, few hormone-dependent enhancers have been characterized and important aspects of their sequence architecture, cell type-specific activating and repressing functions, or the regulatory roles of their chromatin structure have remained unclear. We used STARR-seq, a recently developed enhancer-screening assay, and ecdysone signaling in two different Drosophila cell types to derive the first genome-wide hormone-dependent enhancer activity maps. We demonstrate that enhancer activation depends on cis-regulatory motif combinations that differ between cell types and can predict cell type-specific ecdysone targeting. Activated enhancers are often not accessible prior to induction. Enhancer repression following hormone treatment is independent of receptor motifs and receptor binding to the enhancer as we show using ChIP-seq, but appears to rely on motifs for other factors, including Eip74. Our strategy is applicable to study signal-dependent enhancers for different pathways and across organisms. STARR-seq was performed in S2 and OSC cells treated with ecdysone in two replicates. DHS-seq before and after treatment was done with single-end sequencing in two replicates. RNA-seq (with and without ecdysone) was performed with a strand-specific protocol using single-end sequencing in two replicates in S2. ChIP-seq (with and without ecdysone) was performed single-end sequencing in two replicates in S2 cells.
2014-03-27 | E-GEOD-47691 | biostudies-arrayexpress
Project description:The subject of the current study is the finding of possible molecular partners of Drosophila EcR receptor. Two labelling enzymes (BioID2 and APEX2) were fused to EcR or Usp to biotin label the surrounding proteins. All fused proteins were expressed using the Act5C promoter in Drosophila S2 cells. To ensure functionality of the generated proteins, we verified their ability to bind EcR and Usp sites in the Drosophila genome with the ChIP-Seq. Our results demonstrate that EcR and Usp fusions can be recruited to genomic sites endogenous for the EcR/Usp proteins. Conversely, unfused BioID2 and APEX2 enzymes do not bind to EcR/Usp sites. A more in-depth study was conducted to clarify the association of EcR/Usp with one of the detected proteins, CP190, a well-described cofactor of Drosophila insulators. ChIP-Seq experiments revealed an enrichment of CP190 binding on transcription start and end sites of 20E-dependent genes but not at EcR/Usp-bound enhancers.
2020-03-17 | GSE139316 | GEO