Pilot testing and optimization of a larval fathead minnow high throughput transcriptomics assay
Ontology highlight
ABSTRACT:
ORGANISM(S): Pimephales promelas
PROVIDER: GSE207231 | GEO | 2023/01/01
REPOSITORIES: GEO
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Project description:Characterization of the renal transcriptomic response to Yersinia ruckeri/Conseuqences of early life stage thyroid suppression on long-term immune function and the immune response in the fathead minnow (Pimephales promelas)
2020-05-19 | GSE146105 | GEO
Project description:Nanoparticles are compounds of emerging concern with largely unknown risks for human and ecological health. It is crucial to evaluate their potential biological impact to prevent unintended adverse effects on human health and the environment. We analyzed the transcriptional effects of polyvinylpyrrolidone-coated silver nanoparticles (PVP-AgNPs) and silver nitrate (AgNO3) on the fathead minnow (Pimephales promelas) to understand their potential toxicity and adverse outcomes. We also tested the feasibility of the fathead minnow as an alternative species to elucidate potential adverse effects on humans. Fathead minnow females were exposed to either 4 µg/L of AgNO3 or 70 µg/L of PVP-AgNPs for 96h. Microarray analyses were performed on liver and brain. Functional analysis identified potential toxicity pathways and molecular initiating events (MIEs) that were confirmed with functional assays. Data suggested that AgNO3 and PVP-AgNPs had both common and distinct transcriptional effects. The nanoparticles were linked to neurotoxicity and oxidative stress, and identified as a dopamine receptor antagonist. Silver nitrate was also identified as a potential neurotoxicant and was confirmed as adrenergic and cannabinoid receptors antagonist. While silver nitrate and PVP-AgNPs were both potential neurotoxicants, they appeared to act through different MIEs. Fathead minnow is a promising alternative species to elucidate potential adverse effects of relevance to human health. We analyzed the transcriptional effects of polyvinylpyrrolidone-coated silver nanoparticles (PVP-AgNPs) and silver nitrate (AgNO3) on the fathead minnow (Pimephales promelas) to understand their potential toxicity and adverse outcomes. FHM were obtained from Aquatic Biosystems (Fort Collins, CO), held in aerated dechlorinated tap water and fed three times daily with Zeigler® AquaTox Feed Gardners, PA, USA). Fathead minnow females were exposed to either 4 µg/L of AgNO3 or 70 µg/L of PVP-AgNPs (Luna Innovations, Blackburn, VA) for 96h at 24°C ± 1 with a 90% water change at 48 hours. Microarray analyses were performed on liver and brain.
2013-11-01 | E-GEOD-46520 | biostudies-arrayexpress
Project description:Omics approaches are broadly used to explore endocrine and toxicity-related pathways and functions. Nevertheless, there is still a significant gap in knowledge in terms of understanding the endocrine system and its numerous connections and intricate feedback loops, especially in non-model organisms. The fathead minnow (Pimephales promelas) is a widely used small fish model for aquatic toxicology and regulatory testing, particularly in North America. A draft genome has been published but the amount of available genomic or transcriptomic information is still far behind that of other more broadly studied species, such as the zebrafish. Here, we surveyed the tissue-specific proteome and transcriptome profiles in adult male fathead minnow. To do so, we generated a draft transcriptome using short and long sequencing reads. We also performed RNA sequencing and proteomics analysis on the telencephalon, hypothalamus, liver, and gut of male fish. The main purpose of this analysis was to generate tissue-specific omics data in order to support future aquatic ecotoxicogenomic and endocrine-related studies as well as to improve our understanding of the fathead minnow as an ecological model.
2018-10-15 | PXD010216 | Pride
Project description:New approach methods (NAMs) can reduce the need for chronic, animal-based toxicity and carcinogenicity bioassays. Here, we apply benchmark dose (BMD) response modeling (BMDExpress 2.3) to transcriptomic data after short-term exposures to three organophosphate pesticides (OPPs) to estimate chronic adverse effect levels in mouse. Specifically, mouse-liver were collected for RNA sequencing after 7-days of exposure, respectively, to several dose-levels of well-known OPPs: fenthion, methidathion and parathion. Transcriptional points-of-departure (TPODs) were compared to chronic, apical points-of-departures (APOD) for each OPP to inform more efficient means of estimating chemical potency and risk. The mouse-liver TPODs for fenthion, methidathion, and parathion were 0.009, 0.093, and 0.046 mg/Kg-day, respectively. These short-term TPODs reflected the relative potencies of the most sensitive, apical effects from the chronic studies with fenthion identified as the most potent OPP. Moreover, the TPODs were 2.3 to 17-fold more sensitive than the chronic APODs for mouse, suggesting utility in using short-term gene response for estimating long-term chemical risk. Further investigation into OPPs’ modes of action identified significant impacts on acetylcholinesterase mRNA abundance (FDR p-value <0.05, |FC|>2) as well as enrichment of canonical pathways (IPA, z-score>|2|) associated with organism death and neurological and immune dysfunctions, which have been known to be affected by OPPs. Despite bioassay-related differences, our results indicate the conservation of key events potentially important to OPPs biological activity and potency across species. While additional research is needed, these results build confidence in using short-term, molecular-based assays for the characterization of toxicity and risk, thereby reducing reliance on chronic, rodent-based studies.
2023-11-13 | GSE240853 | GEO
Project description:Paper Abstract. Extrapolating toxicological sensitivity information across species can require the use of highly conservative safety factors as prescribed by ecological risk assessment protocols. The objective of our study was to use multipule factors to understand the dynamics of stress responses by comparing ecotoxicological, developmental, and genomic data to quantitatively determine the relative sensitivity of two common model aquatic vertebrates to assess the potential for developing refined safety factors among species. Larval (3-d old) zebrafish (Danio rerio) and fathead minnows (Pimephales promelas) were concurrently exposed in 96-h static exposures to the widely-used military energetic compound cyclotrimethylenetrinitramine (RDX). Endpoints assessed included mortality, incidence of vertebral deformities, swimming behavior, and differential gene (transcript) expression. Analytically verified treatment concentrations ranged from 0.9 to 27.7 mg/L RDX. While RDX concentrations prepared for exposures included 0, 0.9, 1.8, 3.5, 7.5, 15.0, and 30.0 mg/L, analytically verified treatment concentrations were 0, 0.88, 1.75, 3.46, 6.96, 13.79, and 27.7 mg/L, respectively. Changes in prepared RDX concentrations and analytically verified treatment concentrations are a result of chemical breakdown, a well known characteristic of RDX Our results indicated a higher sensitivity to RDX in P. promelas than in D. rerio in both mortality (LOECs 13.79 and 27.7 mg/L, respectively) and vertebral deformity (LOECs 13.79 and >13.79, respectively) endpoints. Swimming behavior was assessed in 10 min behavioral trials using Noldus EthoVision® digital tracking software. Swimming behavior trials indicated non-significant trends of decreased velocity, distance moved, and increased meander (change in direction per cm traveled) for P. promelas. No such trends were apparent in D. rerio swimming behavior. A comprehensive genomic analysis is in progress to determine the genes, gene ontology elements, metabolic pathways and metabolic networks affected in common among species in the RDX exposure. Taken as a whole, the ecotoxicological, developmental and genomic results will provide valuable insights into the similarity in response among these fish species to RDX. Three-day-old fathead minnow (FHM, Pimephales promelas) or Zebrafish (ZF, Danio rerio) fry were exposed to either control water or one of six concentrations of RDX (0.9, 1.9, 3.8, 7.5, 15, or 27.7 mg/L) in 96-h exposures. However, microarray analysis was only performed on FHM exposed to 0, 0.9, 1.9, 7.5, or 15 mg/L RDX and ZF exposed to 0, 0.9, 1.9, 3.8, 7.5, or 15 mg/L RDX due to insufficient tissue for microarray analysis due to animal death at the other RDX concentrations. The experimental design was based on the U.S. EPA (2002) acute testing method for P. promelas, test method 2000.0 and included four replicates per treatment with ten fish per replicate. Whole fish (10 fish per replicate) were investigated for differential expression in response to RDX exposure.
2011-02-08 | E-GEOD-27067 | biostudies-arrayexpress
Project description:A growing number of studies have examined transcriptional responses to sex steroids along the hypothalamic-pituitary-gonadal axis in teleost fishes. However, data is are lacking on the molecular signaling cascades that underlie progesterone signaling. The objectives of the present study were to characterize the transcriptional response in the ovary of fathead minnow (Pimephales promelas) (FHM) in response to progesterone (P4) using transcriptomics. Female FHM ovaries were exposed in vitro to 500 ng P4/L. Germinal vesicle migration and breakdown (GVBD) was observed and microarrays were used to identify gene cascades affected by P4. Microarray analysis identified 1,265 differentially expressed transcripts after P4 treatment (p < 0.05). Functional enrichment analysis revealed that transcripts involved in the molecular functions of protein serine/threonine kinase activity, ATP binding, and activity of calcium channels were increased in the female ovary after P4 treatment. There was an overwhelming response of genes involved in structural constituent of ribosome to bethat were down-regulated with P4. There was also evidence for gene changes in steroid and maturation-related transcripts. Pathway analyses identified cell cycle regulation, insulin action, hedgehog, and B cell activation as pathways containing an over-representation of highly regulated transcripts. Significant regulatory sub-networks of P4-mediated transcripts included genes regulated by tumor protein p53 and E2F transcription factor 1, suggesting that downstream expression targets of these two proteins may be preferentially involved in P4-mediated GVBD. These data provide novel insight into the molecular signaling cascades that may underlie P4-signaling in the ovary and identifies genes and processes that may indicate premature GVBD due to environmental pollutants that mimic progestins. 3 control and 4 treatment; biological replicates
2013-07-19 | E-GEOD-43601 | biostudies-arrayexpress
Project description:Frog virus 3 (FV3) and other ranaviruses are responsible for an increasing number of die-offs involving wild, farmed, and captive amphibians, fish, and reptiles. Studies in Lithobates pipiens (Leopard frogs) and Xenopus laevis (African clawed frog) indicate that embryos and tadpoles are more likely to succumb to FV3 infection than adult animals. The heightened susceptibility of embryos and tadpoles to ranaviral disease likely reflects the immaturity of their immune system. To ascertain which elements of the immune system respond to ranavirus infection, we explored cellular transcriptional responses following infection of fathead minnow (Pimephales promelas) cells with either wild type (wt) FV3 or a knock out (KO) mutant targeting the 18kDa immediate early gene (18K). At 8 hr post infection (p.i.), a time when late viral gene expression has begun and host protein synthesis has been inhibited, we observed marked up-regulation of multiple cellular transcripts encoding proteins affecting innate and acquired immune responses. We found 2367 target sequences expressed 4-fold or higher in wt-infected cells versus 530 target sequences that were 4-fold or more downregulated. For example, in cells infected with wt virus, interferon (IFN) transcripts were elevated compared to mock-infected cells, along with those encoding IFN regulatory factors (IRFs), IFN stimulated genes (ISGs) such as Mx and MHC class I, and other immune related gene products such as the interleukins IL-1M-NM-2, IL-8, IL-17C and IL-12. Cells infected with the 18K KO mutant (M-bM-^HM-^F18K) showed generally similar levels of induction although quantitative and qualitative differences were noted. Collectively, these results indicate that ranavirus infection induced expression of multiple cellular genes affecting both innate and acquired immunity. It is likely that induction of various immune-related genes may slow or limit viral infection through the activation of multiple components of the innate immune system and, in a whole animal, enhance the development of acquired immunity and protect from disease. To ascertain which elements of the immune system respond to ranavirus infection, we explored cellular transcriptional responses following infection of fathead minnow (Pimephales promelas) cells with either wild type (wt) FV3 or a knock out (KO) mutant targeting the 18kDa immediate early gene (18K). Replicate confluent monolayers of FHM cells grown on 35 mm dishes were mock-infected or infected with wt- or M-bM-^HM-^F18K-FV3 at a MOI of 10 PFU/cell. At 8 hr p.i., total RNA was isolated from samples RNeasy (Qiagen, Valencia, CA, USA) for microarray analysis. Five or six replicates were used per treatment.
2014-06-01 | E-GEOD-53739 | biostudies-arrayexpress
Project description:A growing number of studies have examined transcriptional responses to sex steroids along the hypothalamic-pituitary-gonadal axis in teleost fishes. However, data is are lacking on the molecular signaling cascades that underlie progesterone signaling. The objectives of the present study were to characterize the transcriptional response in the ovary of fathead minnow (Pimephales promelas) (FHM) in response to progesterone (P4) using transcriptomics. Female FHM ovaries were exposed in vitro to 500 ng P4/L. Germinal vesicle migration and breakdown (GVBD) was observed and microarrays were used to identify gene cascades affected by P4. Microarray analysis identified 1,265 differentially expressed transcripts after P4 treatment (p < 0.05). Functional enrichment analysis revealed that transcripts involved in the molecular functions of protein serine/threonine kinase activity, ATP binding, and activity of calcium channels were increased in the female ovary after P4 treatment. There was an overwhelming response of genes involved in structural constituent of ribosome to bethat were down-regulated with P4. There was also evidence for gene changes in steroid and maturation-related transcripts. Pathway analyses identified cell cycle regulation, insulin action, hedgehog, and B cell activation as pathways containing an over-representation of highly regulated transcripts. Significant regulatory sub-networks of P4-mediated transcripts included genes regulated by tumor protein p53 and E2F transcription factor 1, suggesting that downstream expression targets of these two proteins may be preferentially involved in P4-mediated GVBD. These data provide novel insight into the molecular signaling cascades that may underlie P4-signaling in the ovary and identifies genes and processes that may indicate premature GVBD due to environmental pollutants that mimic progestins.
2013-07-19 | GSE43601 | GEO
Project description:Tissue-based mapping of the fathead minnow (Pimephales promelas) transcriptome and proteome
| PRJNA490512 | ENA
Project description:Nanoparticles are compounds of emerging concern with largely unknown risks for human and ecological health. It is crucial to evaluate their potential biological impact to prevent unintended adverse effects on human health and the environment. We analyzed the transcriptional effects of polyvinylpyrrolidone-coated silver nanoparticles (PVP-AgNPs) and silver nitrate (AgNO3) on the fathead minnow (Pimephales promelas) to understand their potential toxicity and adverse outcomes. We also tested the feasibility of the fathead minnow as an alternative species to elucidate potential adverse effects on humans. Fathead minnow females were exposed to either 4 µg/L of AgNO3 or 70 µg/L of PVP-AgNPs for 96h. Microarray analyses were performed on liver and brain. Functional analysis identified potential toxicity pathways and molecular initiating events (MIEs) that were confirmed with functional assays. Data suggested that AgNO3 and PVP-AgNPs had both common and distinct transcriptional effects. The nanoparticles were linked to neurotoxicity and oxidative stress, and identified as a dopamine receptor antagonist. Silver nitrate was also identified as a potential neurotoxicant and was confirmed as adrenergic and cannabinoid receptors antagonist. While silver nitrate and PVP-AgNPs were both potential neurotoxicants, they appeared to act through different MIEs. Fathead minnow is a promising alternative species to elucidate potential adverse effects of relevance to human health.
2013-11-01 | GSE46520 | GEO