ABSTRACT: Fathead minnow ovary explants were incubated with DHT at 10^-6M for 6, 9, and 12 hours. Estrogen production was significantly increased in these ovaries at all three time points. control 6 hours (n=4), DHT 6 hours (n=5), control 9 hours (n=5), DHT 9 hours (n=5), control 12 hours (n=4), DHT 12 hours (n=4),
Project description:The herbicide linuron is an endocrine disruptor with a suspected anti-androgenic mode of action (MOA) but the complete MOA for LIN is not fully characterized. The objectives of this study were to better characterize the MOA of LIN in the fathead minnow (FHMs) ovary by comparing expression profiles of LIN to dihydrotestosterone (DHT) and flutamide (FLUT), both model compounds with well defined androgenic and anti-androgenic MOAs respectively. Ovarian explants from vitellogenic FHMs were exposed to 10-6 M, 10-7 M, and 10-8 M of DHT, FLUT, and LIN in vitro in a12 hour incubation experiment. Ovary explants exposed to DHT showed a significant increase in E2 production compared to controls but FLUT and LIN did not affect E2 production. Microarray analysis and support vector machine classification revealed that expression patterns of FLUT and LIN in the ovary were more similar to each other compared to DHT and other androgens. Gene set enrichment analysis identified the notch signaling cascade was affected by all three chemicals. DHT down-regulated the WNT-Frizzled pathway while LIN down-regulated angiopoietin receptor signaling and increased biosynthesis of cholesterol. LIN shared 27 expression sub-networks (e.g. beta-3 adrenergic receptor, MAP3K1, interleukin, signlaing) in common with FLUT, and only 4 sub-networks with DHT. A reciprocal gene expression network was constructed using DHT and FLUT data, and the network revealed that steroid metabolism, translation, and DNA replication are potentially regulated through AR signaling. This study characterizes cell pathways associated with E2 production and identifies cell signaling cascades that may be disrupted by ureic-based herbicides in the ovary. 16 samples total; 4 control, 4 DHT, 4 Flutamide, 4 LIN
Project description:The objectives of the study were to determine the effects of progesterone in the male testis. Reproductive fathead minnows were used in the study. Testis at stage 2 and 3 were dissected and testis explants were treated progesterone or no progesterone (10^-6M and 10^-8M) for 12 hours. Androgens were measured and there was a significant increase in testosterone, but not 11-tetotetosterone. Gene expression analysis was performed in the testis which genes were differentially regulated by progesterone. testis explants were treated with 10^-6M progesterone for 12 hours; 6 control and 4 treatment samples
Project description:The aim of this study was to determine the in vitro effects of peroxisome proliferator-activated receptor-beta/delta (PPARβ/δ) ligands on the transcriptomic profile of the LPS-stimulated pig CL in the mid-luteal phase of the estrous cycle using RNA-seq technology. The CL slices were incubated in the presence of LPS or in combination with LPS and the PPARβ/δ agonist-GW0724 (1 μmol/L or 10 μmol/L) or the antagonist-GSK3787 (25 μmol/L). We identified 117 differentially expressed genes after treatment with LPS; 102 and 97 differentially expressed genes after treatment respectively with the PPARβ/δ agonist at a concentration of 1 μmol/L or 10 μmol/L, as well as 88-after treatment with the PPARβ/δ antagonist
Project description:In recent years, the use of FFPE tissue in gene expression microarray (GEM) studies has become a topic of increased interest, because pathology departments worldwide contain an invaluable source of biological disease-specific FFPE- tissue material. Thus far, some published studies on FFPE tissue consider the processed tissue amenable, whereas other studies assert that the tissue is not useful in GEM. In general, pancreatic tissue is known to contain large amounts of nucleases, leading to high turnover rates and degradation of RNA in the tissue. This characteristic, in combination with FFPE processing time and its effect on the tissue, does not make FFPE pancreatic tissue the obvious choice for GEM. The basis for using FFPE pancreatic tissue in RNA-based assays seems suboptimal. Previous GEM studies have used different FFPE tissue types, but GEM studies on FFPE pancreatic tissue have not been published. In most studies, the tissue was specially processed for use with GEMs. Here we demonstrate the usefulness of randomly archived FFPE pancreatic tissues for GEMs. For this purpose we included FFPE pancreatic tissue from patients with congenital hyperinsulinism or insulinoma; In these patients, pancreas resection is performed when medical treatment is not adequate to prevent hyperinsulinemic hypoglycemia or when patients do not respond to medical treatment. Although ribonuclease-rich, we obtained biologically relevant and disease-specific, significant genes; cancer-related genes and genes involved in a) the regulation of insulin secretion and synthesis, b) amino acid metabolism, and c) calcium ion homeostasis. This application may extend the possibilities of gene expression studies to many tissue types, especially in rare diseases, for which fresh frozen tissue is not readily available. A total of 15 samples were included in this study using a 58K chip. 29,134 human 60mer oligonucleotide targets were arrayed on the chips in duplicates. Each chip is hybridized with sample material (labelled with Cy5) from one patient and reference material (labelled with Cy3). Reference material contains pooled RNA from four different cancer cell lines; HeLa (cervical epithelium), SK-BR-3 (mammary gland), HT29 (colon) and A431 (skin) cells. Seven patients with congenital hyperinsulinism (five FFPE and two frozen samples), one patient with insulinoma and five controls were included in the study. Inclusion criteria for controls was that their cause of death was not pancreas-related. Samples were obtained from archived FFPE pancreatic material. The insulinoma sample was included in the study, because the biopsy was originally divided with one part being frozen and the other part being routinely formalin-fixed and paraffin-embedded. In the study we therefore include a frozen insulinoma sample and a FFPE insulinoma sample that was processed in duplicate.
Project description:Gene set and sub-network enrichment analysis provides an integrated approach for identifying gene regulatory networks underlying development. Anuran development is a coordinated process, and levels of mRNA are first dominated by maternally deposited genes, followed by active transcription of embryonic genes as the embryo undergoes morphogenesis and organ formation. The objectives of this study were to characterize early gene regulatory networks underlying Silurana tropicalis development. A custom Agilent 4 x 44 K microarray was developed to characterize networks during early development (1, 17, 36, 96 hpf). Cluster analysis revealed that each stage showed unique gene expression profiles and that 1 hpf was most different than the other three stages. There were > 8000 unique gene probes (p<0.01, FDR = 5%) that were differentially expressed between 1 hpf (2 cell stage) and 17 hpf and > 2000 gene probes differentially expressed between 36 hpf and 96 hpf. Genes higher in abundance (>100-fold) at 1 hpf compared to 17 hpf included oocyte-specific histone RNA stem-loop-binding protein 2, mitogen-activated protein kinase 14, and cyclin B5, suggesting these transcripts are maternally inherited or actively transcribed at fertilization. Gene ontology revealed that genes involved in nucleosome assembly, cell division, pattern specification, neurotransmission, and general metabolism were increasingly regulated throughout development, consistent with active development. In the period between 17-36 hpf, gene networks that play a role in organogenesis and organ function, including those related to the heart (heart morphogenesis, central nervous system (olfactory bulb development, dopamine metabolism), and kidney (renal reabsorption, water balance) were activated while between 36-96 hpf, networks involving in gut development, immune responses, lipid metabolism, hormone signaling, and brain development were prevalent. This study increases understanding of the spatiotemporal S. tropicalis embryonic development using gene regulatory networks. Gene expression analysis was performed with four biological replicates for four developmental stages (n = 16). Stages were NF stages 2, 16, 34, and 46.
Project description:We used comparative RNA hybridization (Affymetrix) analysis between Bone metastatic derivatives isolated in vivo and parental cells and focused on changes affecting the expression of potential bone metastasis genes. Total RNA from biological and technical replicates of parental MCF7 and BoM2 bone metastasis derivatives grown for 48 hours in regular media (see growth protocol) was isolated from in vitro cultured control and MAF expressing MCF7 parental cells. Total RNA was extracted using the TRIzolM-BM-. Plus RNA Purification Kit (Life Technologies).
Project description:To identify relevant genes transcriptionally controlled by MAF in breast cancer, we focused on genes whose expression changed accordingly to MAF transcriptiion factor overexpression in MCF7. We used comparative RNA hybridization (Affymetrix) to this end. Total RNA from parental and MAFshort or long isoform overexpressing MCF7 grown for 48 hours in regular media (see growth protocol) was isolated from in vitro cultured control and MAF expressing MCF7 parental cells. Total RNA was extracted using the TRIzolM-BM-. Plus RNA Purification Kit (Life Technologies).
Project description:Transcriptome of A. nidulans TNO2a3 and M-bM-^HM-^FptpB strains when grown on minimal media plus casaminoacids and transferred to minimal media plus glucose as a sole carbon source for 4 hours Three conditions minimal media plus casaminoacids during 24 hours (reference) and minimal media plus glucose for 4 hours. Three strains TNO2a3 and M-bM-^HM-^FptpB. Three biological repetitions of each timepoint of TNO2a3 / M-bM-^HM-^FptpB
Project description:Considering the well-documented importance of androgens in the female reproductive system and particularly in maintenance of the ovarian follicular reserve, follicle growth and granulosa cell proliferation, we hypothesized that activation of the androgen receptor in granulosa cells with DHT induces significant changes in gene transcription. To determine the AR-regulated gene transcriptome in mouse granulosa cells, we treated female mice aged 18 weeks (n=5) with an introperitoneal injection of dihydrotestosterone (DHT, 29 mcg) in a vehicle of 90% sesame oil and 10% ethanol in a total volume of 100 microliters. 18 hours later, granulosa cells were harvested and mRNA was isolated for RNA sequencing. Surprisingly, no genes were differentially expressed in the granulosa cells obtained from DHT-treated compared with vehicle-treated mice. We then assessed the AR-regulated transcriptome in DHT-treated human granulosa-derived KGN cells. After 24 hours of serum starvation, KGN cells were treated with 25 nM DHT or ethanol for 12 hours in five independent experiments, then RNA was extracted for RNA sequencing. In paired analysis to eliminate inter-experimental variability, 173 genes were differentially expressed in DHT-treated compared with vehicle-treated cells. Of these, 125 genes were upregulated by DHT and 48 genes were downregulated by DHT. However, the fold change in expression was very small (ranging from 0.87 to 1.37, DHT vs vehicle). Although these differences were statistically signficant in paired analysis, they are unlikely to be of biological significance due to such small fold changes in expression. We conclude that AR likely has negligible gene-transcription activity in granulosa cells. Importantly, these experiments were not designed to capture any changes in non-coding RNAs.
Project description:Expression data from DHT stimulation vs. control in LNCaP cells LNCaP cells were maintained in phenol red-free RPMI supplemented with 10% charcoal/dextran stripped FCS for three days before stimulation with 100 nM dihydrotestosterone (DHT) for 48 hours